Endophytes and related methods

ABSTRACT

The present invention relates to a method for identifying and/or characterising an endophyte strain, said method including providing a plurality of samples of endophytes, subjecting said endophytes to genetic analysis, subjecting said endophytes to metabolic analysis and selecting endophytes having a desired genetic and metabolic profile. 
     The present invention also relates to novel endophytes having a desired toxin profile wherein the endophyte produces significantly less toxic alkaloids compared with a control endophyte such as standard toxic (ST) endophyte; and/or significantly more alkaloids conferring beneficial properties compared with a control endophyte such as ST endophyte. 
     The present invention also relates to endophyte variants having a desired genetic and metabolic profile, wherein said endophyte variants possess genetic and/or metabolic characteristics that result in a beneficial phenotype in a plant harbouring or otherwise associated with the endophyte variant. Preferably said endophyte variants are generated by polyploidisation or induced chromosome doubling.

STATEMENT OF RELATED CASES

This application is a continuation in part of PCT/AU2011/000020, filed Jan. 7, 2011, which claims priority from Australian Patent Application 2010900054 filed Jan. 7, 2010, and Australian Patent Application 2010902821, filed Jun. 25, 2010, and also claims priority from Australian Patent Application Nos. 2012902275 and 2012902276, filed Jun. 1, 2012. All of these applications are incorporated herein by reference in their entirety.

FIELD OF THE INVENTION

The present invention relates to endophytic fungi (endophytes), including modified variants thereof, and to nucleic acids thereof. The present invention also relates to plants infected with endophytes and to related methods, including methods of selecting, breeding, characterising and/or modifying endophytes.

BACKGROUND OF THE INVENTION

Important forage grasses perennial ryegrass and tall fescue are commonly found in association with fungal endophytes.

Both beneficial and detrimental agronomic properties result from the association, including improved tolerance to water and nutrient stress and resistance to insect pests.

Insect resistance is provided by specific metabolites produced by the endophyte, in particular loline alkaloids and peramine. Other metabolites produced by the endophyte, lolitrems and ergot alkaloids, are toxic to grazing animals and reduce herbivore feeding.

Considerable variation is known to exist in the metabolite profile of endophytes. Endophyte strains that lack either or both of the animal toxins have been introduced into commercial cultivars.

Molecular genetic markers such as simple sequence repeat (SSR) markers have been developed as diagnostic tests to distinguish between endophyte taxa and detect genetic variation within taxa. The markers may be used to discriminate endophyte strains with different toxin profiles.

However, there remains a need for methods of identifying, isolating, characterising and/or modifying endophytes and a need for new endophyte strains having desired properties.

In the fungal kingdom, there is no differentiation of individuals into sexes generating different gametes, but instead mating-type identity is determined by inheritance of alleles at specific mating-type loci.

The mating-type (MAT) genes constitute master regulators of sexual reproduction in filamentous fungi. Although mating-type loci consist of one to a few linked genes, and are thus limited to a small genomic region, alternate sequences at MAT, denoted idiomorphs, lack significant sequence similarity and encode different transcriptional regulators.

Fusion events are required during sexual reproduction in filamentous ascomycete species. Although cell fusion processes associated with vegetative growth as opposed to sexual development serve different developmental functions, both require extracellular communication and chemotropic interactions, followed by cell wall breakdown, membrane-merger and pore formation.

A number of genes have been characterised that are required for both sexual reproduction and vegetative hyphal fusion, including components of the MAPK pathway which is activated in response to pheromone perception during mating. The expression of pheromone precursors and pheromone receptor genes is directly controlled by transcription factors encoded by the mating-type genes.

Hyphal fusion occurs readily within an individual colony during vegetative growth, maintaining the physiological continuity of the organism. Hyphal fusion between different endophyte strains of opposite mating-type may be promoted by treating the mycelia with a combination of cell wall-degrading enzymes and fusion agents such as PEG4000.

However, there remains a need for methods of molecular breeding of endophytes and for new endophyte strains having desired properties.

Neotyphodium endophytes are not only of interest in agriculture, as they are a potential source for bioactive molecules such as insecticides, fungicides, other biocides and bioprotectants, allelochemicals, medicines and nutraceuticals.

Difficulties in artificially breeding of these endophytes limit their usefulness. For example, many of the novel endophytes known to be beneficial to pasture-based agriculture exhibit low inoculation frequencies and are less stable in elite germplasm.

Thus, there remains a need for methods of generating novel, highly compatible endophytes.

There also remains a need for more endophyte strains with desirable properties and for more detailed characterisation of their toxin and metabolic profiles, antifungal activity, stable host associations and their genomes.

It is an object of the present invention to overcome, or at least alleviate, one or more of the difficulties or deficiencies associated with the prior art.

In a first aspect, the present invention provides a method for selecting and/or characterising an endophyte strain, said method including:

-   -   providing a plurality of samples of endophytes;     -   subjecting said endophytes to genetic analysis;     -   subjecting said endophytes to metabolic analysis; and     -   selecting endophytes having a desired genetic and metabolic         profile.

In a preferred embodiment, this aspect of the invention may include the further step of assessing geographic origin of the endophytes and selecting endophytes having a desired genetic and metabolic profile and a desired geographic origin.

In a preferred embodiment, the plurality of samples of endophytes may be provided by a method including:

-   -   providing a plurality of plant samples; and     -   isolating endophytes from said plant samples.

In a preferred embodiment, the method may be performed using an electronic device, such as a computer.

Applicant has surprisingly found that specific detection of endophytes in planta with markers such as SSR markers has provided the tools for efficient assessment of endophyte genetic diversity in diverse grass populations and the potential discovery of novel endophyte strains.

A large scale endophyte discovery program was undertaken to establish a ‘library’ of novel endophyte strains. A collection of perennial ryegrass and tall fescue accessions was established.

Genetic analysis of endophytes in these accessions has lead to the identification of a number of novel endophyte strains. These novel endophyte strains are genetically distinct from known endophyte strains.

Metabolic profiling was undertaken to determine the toxin profile of these strains grown in vitro and/or following inoculation in planta.

Specific detection of endophytes in planta with SSR markers may be used to confirm the presence and identity of endophyte strains artificially inoculated into, for example, grass plants, varieties and cultivars.

The endophytes have been genetically characterised to demonstrate genetic distinction from known endophyte strains and to confirm the identity of endophyte strains artificially inoculated into, for example, grass plants, varieties and cultivars.

By a ‘plurality’ of samples of endophytes or plant samples is meant a number sufficient to enable a comparison of genetic and metabolic profiles of individual endophytes.

Preferably, between approximately 10 and 1,000,000 endophytes are provided, more preferably between approximately 100 and 1,000 endophytes.

Phenotypic screens were established to select for novel ‘designer’ grass-endophyte associations. These screens were for desirable characteristics such as enhanced biotic stress tolerance, enhance drought tolerance and enhanced water use efficiency, and enhanced plant vigour.

Novel ‘designer’ endophytes were generated by targeted methods including polyploidisation and X-ray mutagenesis.

These endophytes may be characterised, for example using antifungal bioassays, in vitro growth rate assays and/or genome survey sequencing (GSS).

Metabolic profiling may also be undertaken to determine the toxin profile of these strains grown in vitro and/or following inoculation in planta.

These endophytes may be delivered into plant germplasm to breed ‘designer’ grass endophyte associations.

Specific detection of endophytes in planta with SSR markers may be used to confirm the presence and identity of endophyte strains artificially inoculated into, for example, grass plants, varieties and cultivars.

The endophytes may be subject to genetic analysis (genetically characterized) to demonstrate genetic distinction from known endophyte strains and to confirm the identity of endophyte strains artificially inoculated into, for example, grass plants, varieties and cultivars.

By ‘genetic analysis’ is meant analysing the nuclear and/or mitochondrial DNA of the endophyte.

This analysis may involve detecting the presence or absence of polymorphic markers, such as simple sequence repeats (SSRs) or mating-type markers. SSRs, also called microsatellites, are based on a 1-7 nucleotide core element, more typically a 1-4 nucleotide core element, that is tandemly repeated. The SSR array is embedded in complex flanking DNA sequences. Microsatellites are thought to arise due to the property of replication slippage, in which the DNA polymerase enzyme pauses and briefly slips in terms of its template, so that short adjacent sequences are repeated. Some sequence motifs are more slip-prone than others, giving rise to variations in the relative numbers of SSR loci based on different motif types. Once duplicated, the SSR array may further expand (or contract) due to further slippage and/or unequal sister chromatid exchange. The total number of SSR sites is high, such that in principle such loci are capable of providing tags for any linked gene.

SSRs are highly polymorphic due to variation in repeat number and are co-dominantly inherited. Their detection is based on the polymerase chain reaction (PCR), requiring only small amounts of DNA and suitable for automation. They are ubiquitous in eukaryotic genomes, including fungal and plant genomes, and have been found to occur every 21 to 65 kb in plant genomes. Consequently, SSRs are ideal markers for a broad range of applications such as genetic diversity analysis, genotypic identification, genome mapping, trait mapping and marker-assisted selection.

Known SSR markers which may be used to investigate endophyte diversity in perennial ryegrass are described in van Zijll de Jong et al (2003).

Alternatively, or in addition, the genetic analysis may involve sequencing genomic and/or mitochondrial DNA and performing sequence comparisons to assess genetic variation between endophytes.

The endophytes may be subject to metabolic analysis to identify the presence of desired metabolic traits.

By ‘metabolic analysis’ is meant analysing metabolites, in particular toxins, produced by the endophytes. Preferably, this is done by generation of inoculated plants for each of the endophytes and measurement of toxin levels in planta. More preferably, this is done by generation of isogenically inoculated plants for each of the endophytes and measurement of toxin levels in planta.

By a ‘desired genetic and metabolic profile’ is meant that the endophyte includes genetic and metabolic characteristics that result in a beneficial phenotype in a plant harbouring, or otherwise associated with, the endophyte.

Such beneficial properties include improved tolerance to water and/or nutrient stress, improved resistance to pests and/or diseases, enhanced biotic stress tolerance, enhanced drought tolerance, enhanced water use efficiency, reduced toxicity and enhanced vigour in the plant with which the endophyte is associated, relative to a control endophyte such as standard toxic (ST) endophyte or to a no endophyte control plant.

For example, tolerance to water and/or nutrient stress may be increased by at least approximately 5%, more preferably at least approximately 10%, more preferably at least approximately 25%, more preferably at least approximately 50%, more preferably at least approximately 100%, relative to a control endophyte such as standard toxic (ST) endophyte or to no endophyte control plant. Preferably, tolerance to water and/or nutrient stress may be increased by between approximately 5% and approximately 50%, more preferably between approximately 10% and approximately 25%, relative to a control endophyte such as ST or to a no endophyte control plant.

Such beneficial properties also include reduced toxicity of the associated plant to grazing animals.

For example, toxicity may be reduced by at least approximately 5%, more preferably at least approximately 10%, more preferably at least approximately 25%, more preferably at least approximately 50%, more preferably at least approximately 100%, relative to a control endophyte such as ST endophyte. Preferably, toxicity may be reduced by between approximately 5% and approximately 100%, more preferably between approximately 50% and approximately 100% relative to a control endophyte such as ST endophyte.

In a preferred embodiment toxicity may be reduced to a negligible amount or substantially zero toxicity.

For example, water use efficiency and/or plant vigour may be increased by at least approximately 5%, more preferably at least approximately 10%, more preferably at least approximately 25%, more preferably at least approximately 50%, more preferably at least approximately 100%, relative to a control endophyte such as ST or to a no endophyte control plant. Preferably, tolerance to water and/or nutrient stress may be increased by between approximately 5% and approximately 50%, more preferably between approximately 10% and approximately 25%, relative to a control endophyte such as ST or to a no endophyte control plant.

The methods of the present invention may be applied to a variety of plants. In a preferred embodiment, the methods may be applied to grasses, preferably forage, turf or bioenergy grasses such as those of the genera Lolium and Festuca, including L. perenne (perennial ryegrass) and L. arundinaceum (tall fescue).

The methods of the present invention may be applied to a variety of endophytes. In a preferred embodiment, the methods may be applied to fungi of the genus Neotyphodium, including N. lolii and N. coenophialum. In another preferred embodiment, the methods may be applied to fungi of the genus Epichloë, including E. festucae and E. typhina. However, the methods may also be used to identify endophytes of previously undescribed taxa.

Applicants have surprisingly found that endophyte E1 is a genetically novel, non-Neotyphodium lolii, endophyte. E1 is representative of an as yet un-named taxon. This finding is supported by mitochondrial and nuclear genome sequence analysis.

While applicants do not wish to be restricted by theory, on the basis of DNA specific content, the predicted alkaloid profile of E1 indicates that lolitrem B toxins deleterious to animal health are not produced by this endophyte. Endophyte E1 has the mating-type MAT1-1, the opposite mating-type to that carried by the N. lolii endophytes previously characterized. Endophyte E1 also has a high inoculation success rate in perennial ryegrass as compared to other endophytes.

Accordingly, in a second aspect, the present invention provides a substantially purified or isolated endophyte selected from the group consisting of E1, NEA10, NEA11 and NEA12, which were deposited at The National Measurement Institute, 1/153 Bertie Street, Port Melbourne, Victoria, Australia, 3207, on 5 Jan. 2010 with accession numbers V10/000001, V10/000002, V10/000003 and V10/000004, respectively. Replacement deposits were made on Apr. 15, 2016 in response to a notification of non-viability, and were assigned the same accession numbers.

The present invention also provides a substantially purified or isolated endophyte selected from the group consisting of NEA13 and NEA14, which were deposited at the National Measurement Institute, 1/153 Bertie Street, Port Melbourne, Victoria, Australia, 3207, on 23 Dec. 2010 with accession numbers V10/030285 and V10/030284, respectively. Replacement deposits were made on Apr. 15, 2016 in response to a notification of non-viability, and were assigned the same accession numbers.

In a further aspect the present invention provides a substantially purified or isolated endophyte having a desired toxin profile. Preferably the endophyte is isolated from a fescue species, preferably tall fescue. Preferably, the endophyte is of the genus Neotyphodium, more preferably it is from a species selected from the group consisting of N. uncinatum, N. coenophialum and N. lolii, most preferably N. coenophialum. The endophyte may also be from the genus Epichloe, including E. typhina, E. baconii and E. festucae. The endophyte may also be of the non-Epichloe out-group. The endophyte may also be from a species selected from the group consisting of FaTG-3 and FaTG-3 like, and FaTG-2 and FaTG-2 like.

By a ‘desired toxin profile’ is meant that the endophyte produces significantly less toxic alkaloids, such as ergovaline, compared with a plant inoculated with a control endophyte such as standard toxic (ST) endophyte; and/or significantly more alkaloids conferring beneficial properties such as improved tolerance to water and/or nutrient stress and improved resistance to pests and/or diseases in the plant with which the endophyte is associated, such as peramine, N-formylloline, N-acetylloline and norloline, again when compared with a plant inoculated with a control endophyte such as ST or with a no endophyte control plant.

For example, toxic alkaloids may be present in an amount less than approximately 11.1 g/g dry weight, for example between approximately 1 and 0.001 μg/g dry weight, preferably less than approximately 0.5 μg/g dry weight, for example between approximately 0.5 and 0.001 μg/g dry weight, more preferably less than approximately 0.2 μg/g dry weight, for example between approximately 0.2 and 0.001 μg/g dry weight.

For example, said alkaloids conferring beneficial properties may be present in an amount of between approximately 5 and 100 μg/g dry weight, preferably between approximately 10 and 50 μg/g dry weight, more preferably between approximately 15 and 30 μg/g dry weight.

In a particularly preferred embodiment, the present invention provides a substantially purified or isolated endophyte selected from the group consisting of NEA16, NEA17, NEA18, NEA19, NEA20, NEA21 and NEA23, which were deposited at The National Measurement Institute, 1/153 Bertie Street, Port Melbourne, Victoria, Australia, 3207, on 3 Apr. 2012 with accession numbers V12/001413, V12/001414, V12/001415, V12/001416, V12/001417, V12/001418 and V12/001419, respectively. Replacement deposits were made on Apr. 15, 2016 in response to a notification of non-viability, and were assigned the same accession numbers. Such endophytes may have a desired toxin profile as hereinbefore described.

In a further aspect the present invention provides an endophyte variant having a desired genetic and metabolic profile. Preferably the endophyte variant is generated by polyploidisation or induced chromosome doubling, for example by treating the endophyte with colchicine or a similar compound. Alternatively, the endophyte variant may be generated by X-ray mutagenesis or exposing the endophyte to ionising radiation, for example from a caesium source.

Preferably the endophyte which is treated to generate the endophyte variant is isolated from a Lolium species, preferably Lolium perenne. Preferably, the endophyte is of the genus Neotyphodium, more preferably it is from a species selected from the group consisting of N uncinatum, N coenophialum and N lolii, most preferably N lolii. The endophyte may also be from the genus Epichloe, including E typhina, E baconii and E festucae. The endophyte may also be of the non-Epichloe out-group. The endophyte may also be from a species selected from the group consisting of FaTG-3 and FaTG-3 like, and FaTG-2 and FaTG-2 like.

In a preferred embodiment, the endophyte variant may have a desired toxin profile. By a ‘desired toxin profile’ is meant that the endophyte produces significantly less toxic alkaloids, such as ergovaline, compared with a plant inoculated with a control endophyte such as standard toxic (ST) endophyte; and/or significantly more alkaloids conferring beneficial properties such as improved resistance to pests and/or diseases in the plant with which the endophyte is associated, such as peramine, N-formylloline, N-acetylloline and norloline, again when compared with a plant inoculated with a control endophyte such as ST or with a no endophyte control plant.

For example, toxic alkaloids may be present in an amount less than approximately 11.1 g/g dry weight, for example between approximately 1 and 0.001 μg/g dry weight, preferably less than approximately 0.5 μg/g dry weight, for example between approximately 0.5 and 0.001 μg/g dry weight, more preferably less than approximately 0.2 μg/g dry weight, for example between approximately 0.2 and 0.001 μg/g dry weight.

For example, said alkaloids conferring beneficial properties may be present in an amount of between approximately 5 and 100 μg/g dry weight, preferably between approximately 10 and 50 μg/g dry weight, more preferably between approximately 15 and 30 μg/g dry weight.

In a particularly preferred embodiment, the present invention provides an endophyte variant selected from the group consisting of NEA12dh5, NEA12dh6, NEA12dh13, NEA12dh14, and NEA12dh17, which were deposited at The National Measurement Institute, 1/153 Bertie Street, Port Melbourne, Victoria, Australia, 3207, on 3 Apr. 2012 with accession numbers V12/001408, V12/001409, V12/001410, V12/001411 and V12/001412, respectively. Replacement deposits were made on Apr. 15, 2016 in response to a notification of non-viability, and were assigned the same accession numbers. Such endophytes may have a desired genetic and metabolic profile as hereinbefore described.

In a preferred embodiment, the endlphyte may be substantially purified.

By ‘substantially purified’ is meant that the endophyte is free of other organisms. The term therefore includes, for example, an endophyte in axenic culture. Preferably, the endophyte is at least approximately 90% pure, more preferably at least approximately 95% pure, even more preferably at least approximately 98% pure.

The term ‘isolated’ means that the endophyte is removed from its original environment (eg. the natural environment if it is naturally occurring). For example, a naturally occurring endophyte present in a living plant is not isolated, but the same endophyte separated from some or all of the coexisting materials in the natural system, is isolated.

On the basis of the deposits referred to above, the entire genome of an endophyte selected from the group consisting of E1, NEA10, NEA11, NEA12, NEA13, NEA14, NEA21, NEA23, NEA18, NEA19, NEA16, NEA20, NEA12dh5, NEA12dh6, NEA12dh13, NEA12dh14 and NEA12dh17, is incorporated herein by reference.

Thus, in a further aspect, the present invention includes identifying and/or cloning nucleic acids including genes encoding polypeptides or transcription factors, for example transcription factors that are involved in sexual reproduction or vegetative hyphal fusion, in an endophyte. For example, the nucleic acids may encode mating-type genes, such as MAT1-1.

Methods for identifying and/or cloning nucleic acids encoding such genes are known to those skilled in the art and include creating nucleic acid libraries, such as cDNA or genomic libraries, and screening such libraries, for example using probes for genes of the desired type, for example mating-type genes; or mutating the genome of the endophyte of the present invention, for example using chemical or transposon mutagenesis, identifying changes in the production of polypeptides or transcription factors of interest, for example those that are involved in sexual reproduction or vegetative hyphal fusion, and thus identifying genes encoding such polypeptides or transcription factors.

Thus, in a further aspect of the present invention, there is provided a substantially purified or isolated nucleic acid encoding a polypeptide or transcription factor from the genome of an endophyte of the present invention. Preferably, the nucleic acid may encode a polypeptide or transcription factor that is involved in sexual reproduction or vegetative hyphal fusion in an endophyte.

In a preferred embodiment, the nucleic acid may include a mating-type gene, such as MAT1-1, or a functionally active fragment or variant thereof.

In a particularly preferred embodiment, the nucleic acid may include a nucleotide sequence selected from the group consisting of sequences shown in FIG. 1 hereto, and functionally active fragments and variants thereof.

By ‘nucleic acid’ is meant a chain of nucleotides capable of carrying genetic information. The term generally refers to genes or functionally active fragments or variants thereof and or other sequences in the genome of the organism that influence its phenotype. The term ‘nucleic acid’ includes DNA (such as cDNA or genomic DNA) and RNA (such as mRNA or microRNA) that is single- or double-stranded, optionally containing synthetic, non-natural or altered nucleotide bases, synthetic nucleic acids and combinations thereof.

By a ‘nucleic acid encoding a polypeptide or transcription factor’ is meant a nucleic acid encoding an enzyme or transcription factor normally present in an endophyte of the present invention.

By a ‘nucleic acid encoding a polypeptide or transcription factor involved sexual reproduction or vegetative hyphal fusion’ is meant a nucleic acid encoding an enzyme or transcription factor normally present in an endophyte of the present invention, which catalyses or regulates a step involved in sexual reproduction or vegetative hyphal fusion in the endophyte, or otherwise regulates sexual reproduction or vegetative hyphal fusion in the endophyte.

The present invention encompasses functionally active fragments and variants of the nucleic acids of the present invention. By ‘functionally active’ in relation to the nucleic acid is meant that the fragment or variant (such as an analogue, derivative or mutant) is capable of manipulating the function of the encoded polypeptide, for example by being translated into an enzyme or transcription factor that is able to catalyse or regulate a step involved in the relevant pathway, or otherwise regulate the pathway in the endophyte. For example, the fragment or variant may be capable of manipulating sexual reproduction or vegetative hyphal fusion in an endophyte, for example by being translated into an enzyme or transcription factor that is able to catalyse or regulate a step involved in sexual reproduction or vegetative hyphal fusion in the endophyte, or otherwise regulate sexual reproduction or vegetative hyphal fusion in the endophyte.

Such variants include naturally occurring allelic variants and non-naturally occurring variants. Additions, deletions, substitutions and derivatizations of one or more of the nucleotides are contemplated so long as the modifications do not result in loss of functional activity of the fragment or variant. Preferably the functionally active fragment or variant has at least approximately 80% identity to the relevant part of the above mentioned sequence to which the fragment or variant corresponds, more preferably at least approximately 90% identity, even more preferably at least approximately 95% identity, most preferably at least approximately 98% identity. Such functionally active variants and fragments include, for example, those having conservative nucleic acid changes. Examples of suitable nucleic acid changes are also shown in FIG. 1 hereto.

Preferably the fragment has a size of at least 20 nucleotides, more preferably at least 50 nucleotides, more preferably at least 100 nucleotides.

By ‘conservative nucleic acid changes’ is meant nucleic acid substitutions that result in conservation of the amino acid in the encoded protein, due to the degeneracy of the genetic code. Such functionally active variants and fragments also include, for example, those having nucleic acid changes which result in conservative amino acid substitutions of one or more residues in the corresponding amino acid sequence.

By ‘conservative amino acid substitutions’ is meant the substitution of an amino acid by another one of the same class, the classes being as follows:

-   -   Nonpolar: Ala, Val, Leu, Ile, Pro, Met, Phe, Trp     -   Uncharged polar: Gly, Ser, Thr, Cys, Tyr, Asn, Gln     -   Acidic: Asp, Glu     -   Basic: Lys, Arg, His

Other conservative amino acid substitutions may also be made as follows:

-   -   Aromatic: Phe, Tyr, His     -   Proton Donor: Asn, Gln, Lys, Arg, His, Trp     -   Proton Acceptor: Glu, Asp, Thr, Ser, Tyr, Asn, Gln

In a further aspect of the present invention, there is provided a genetic construct including a nucleic acid according to the present invention.

By ‘genetic construct’ is meant a recombinant nucleic acid molecule.

In a preferred embodiment, the genetic construct according to the present invention may be a vector.

By a ‘vector’ is meant a genetic construct used to transfer genetic material to a target cell.

The vector may be of any suitable type and may be viral or non-viral. The vector may be an expression vector. Such vectors include chromosomal, non-chromosomal and synthetic nucleic acid sequences, eg. derivatives of plant viruses; bacterial plasmids; derivatives of the Ti plasmid from Agrobacterium tumefaciens; derivatives of the Ri plasmid from Agrobacterium rhizogenes; phage DNA; yeast artificial chromosomes; bacterial artificial chromosomes; binary bacterial artificial chromosomes; vectors derived from combinations of plasmids and phage DNA. However, any other vector may be used as long as it is replicable or integrative or viable in the target cell.

In a preferred embodiment of this aspect of the invention, the genetic construct may further include a promoter and a terminator; said promoter, gene and terminator being operatively linked.

By a ‘promoter’ is meant a nucleic acid sequence sufficient to direct transcription of an operatively linked nucleic acid sequence.

By ‘operatively linked’ is meant that the nucleic acid(s) and a regulatory sequence, such as a promoter, are linked in such a way as to permit expression of said nucleic acid under appropriate conditions, for example when appropriate molecules such as transcriptional activator proteins are bound to the regulatory sequence. Preferably an operatively linked promoter is upstream of the associated nucleic acid.

By ‘upstream’ is meant in the 3′->5′ direction along the nucleic acid.

The promoter and terminator may be of any suitable type and may be endogenous to the target cell or may be exogenous, provided that they are functional in the target cell.

A variety of terminators which may be employed in the genetic constructs of the present invention are also well known to those skilled in the art. The terminator may be from the same gene as the promoter sequence or a different gene. Particularly suitable terminators are polyadenylation signals, such as the (CaMV)35S polyA and other terminators from the nopaline synthase (nos) and the octopine synthase (ocs) genes.

The genetic construct, in addition to the promoter, the gene and the terminator, may include further elements necessary for expression of the nucleic acid, in different combinations, for example vector backbone, origin of replication (ori), multiple cloning sites, spacer sequences, enhancers, introns (such as the maize Ubiquitin Ubi intron), antibiotic resistance genes and other selectable marker genes [such as the neomycin phosphotransferase (nptII) gene, the hygromycin phosphotransferase (hph) gene, the phosphinothricin acetyltransferase (bar or pat) gene], and reporter genes [such as beta-glucuronidase (GUS) gene (gusA) and the green fluorescent protein (GFP) gene (gfp)]. The genetic construct may also contain a ribosome binding site for translation initiation. The genetic construct may also include appropriate sequences for amplifying expression.

Those skilled in the art will appreciate that the various components of the genetic construct are operably linked, so as to result in expression of said nucleic acid. Techniques for operably linking the components of the genetic construct of the present invention are well known to those skilled in the art. Such techniques include the use of linkers, such as synthetic linkers, for example including one or more restriction enzyme sites.

Preferably, the genetic construct is substantially purified or isolated.

By ‘substantially purified’ is meant that the genetic construct is free of the genes, which, in the naturally-occurring genome of the organism from which the nucleic acid or promoter of the invention is derived, flank the nucleic acid or promoter. The term therefore includes, for example, a genetic construct which is incorporated into a vector; into an autonomously replicating plasmid or virus; or into the genomic DNA of a prokaryote or eukaryote; or which exists as a separate molecule (eg. a cDNA or a genomic or cDNA fragment produced by PCR or restriction endonuclease digestion) independent of other sequences. It also includes a genetic construct which is part of a hybrid gene encoding additional polypeptide sequence.

Preferably, the substantially purified genetic construct is at least approximately 90% pure, more preferably at least approximately 95% pure, even more preferably at least approximately 98% pure.

The term “isolated” means that the material is removed from its original environment (eg. the natural environment if it is naturally occurring). For example, a naturally occurring nucleic acid present in a living plant is not isolated, but the same nucleic acid separated from some or all of the coexisting materials in the natural system, is isolated. Such nucleic acids could be part of a vector and/or such nucleic acids could be part of a composition, and still be isolated in that such a vector or composition is not part of its natural environment.

As an alternative to use of a selectable marker gene to provide a phenotypic trait for selection of transformed host cells, the presence of the genetic construct in transformed cells may be determined by other techniques well known in the art, such as PCR (polymerase chain reaction), Southern blot hybridisation analysis, histochemical assays (e.g. GUS assays), thin layer chromatography (TLC), northern and western blot hybridisation analyses.

The genetic constructs of the present invention may be introduced into plants or fungi by any suitable technique. Techniques for incorporating the genetic constructs of the present invention into plant cells or fungal cells (for example by transduction, transfection, transformation or gene targeting) are well known to those skilled in the art. Such techniques include Agrobacterium-mediated introduction, Rhizobium-mediated introduction, electroporation to tissues, cells and protoplasts, protoplast fusion, injection into reproductive organs, injection into immature embryos and high velocity projectile introduction to cells, tissues, calli, immature and mature embryos, biolistic transformation, Whiskers transformation, and combinations thereof. The choice of technique will depend largely on the type of plant or fungus to be transformed, and may be readily determined by an appropriately skilled person. For transformation of protoplasts, PEG-mediated transformation is particularly preferred. For transformation of fungi PEG-mediated transformation and electroporation of protoplasts and Agrobacterium-mediated transformation of hyphal explants are particularly preferred.

Cells incorporating the genetic constructs of the present invention may be selected, as described below, and then cultured in an appropriate medium to regenerate transformed plants or fungi, using techniques well known in the art. The culture conditions, such as temperature, pH and the like, will be apparent to the person skilled in the art. The resulting plants or fungi may be reproduced, either sexually or asexually, using methods well known in the art, to produce successive generations of transformed plants or fungi. In a further aspect, the present invention provides a plant inoculated with an endophyte or endophyte variant as hereinbefore described, said plant comprising an endophyte-free host plant stably infected with said endophyte or endophyte variant.

Preferably, the plant is infected with the endophyte or endophyte variant by a method selected from the group consisting of inoculation, breeding, crossing, hybridization and combinations thereof.

In a preferred embodiment, the plant may be infected by isogenic inoculation. This has the advantage that phenotypic effects of endophytes may be assessed in the absence of host-specific genetic effects. More particularly, multiple inoculations of endophytes may be made in plant germplasm, and plantlets regenerated in culture before transfer to soil.

The identification of an endophyte of the opposite mating-type that is highly compatible and stable in planta provides a means for molecular breeding of endophytes for perennial ryegrass. Preferably the plant may be infected by hyper-inoculation.

Hyphal fusion between endophyte strains of the opposite mating-type provides a means for delivery of favourable traits into the host plant, preferably via hyper-inoculation. Such strains are preferably selected from the group including an endophyte strain that exhibits the favourable characteristics of high inoculation frequency and high compatibility with a wide range of germplasm, preferably elite perennial ryegrass and/or tall fescue host germplasm and an endophyte that exhibits a low inoculation frequency and low compatibility, but has a highly favourable alkaloid toxin profile.

It has generally been assumed that interactions between endophyte taxa and host grasses will be species specific. Applicants have surprisingly found that endophyte from tall fescue may be used to deliver favourable traits to ryegrasses, such as perennial ryegrass.

In a further aspect of the present invention there is provided a method of analysing metabolites in a plurality of endophytes, said method including:

-   -   providing:         -   a plurality of endophytes; and         -   a plurality of isogenic plants;     -   inoculating each isogenic plant with an endophyte;     -   culturing the endophyte-infected plants; and     -   analysing the metabolites produced by the endophyte-infected         plants.

By ‘metabolites’ is meant chemical compounds, in particular toxins, produced by the endophyte-infected plant, including, but not limited to, lolines, peramine, ergovaline, lolitrem, and janthitrems, such as janthitrem I, janthitrem G and janthitem F.

By Isogenic plants' is meant that the plants are genetically identical.

The endophyte-infected plants may be cultured by known techniques. The person skilled in the art can readily determine appropriate culture conditions depending on the plant to be cultured.

The metabolites may be analysed by known techniques such as chromatographic techniques or mass spectrometry, for example LCMS or HPLC. In a particularly preferred embodiment, endophyte-infected plants may be analysed by reverse phase liquid chromatography mass spectrometry (LCMS). This reverse phase method may allow analysis of specific metabolites (including lolines, peramine, ergovaline, lolitrem, and janthitrems, such as janthitrem I, janthitrem G and janthitem F) in one LCMS chromatographic run from a single endophyte-infected plant extract.

In another particularly preferred embodiment, LCMS including EIC (extracted ion chromatogram) analysis may allow detection of the alkaloid metabolites from small quantities of endophyte-infected plant material. Metabolite identity may be confirmed by comparison of retention time with that of pure toxins or extracts of endophyte-infected plants with a known toxin profile analysed under substantially the same conditions and/or by comparison of mass fragmentation patterns, for example generated by MS2 analysis in a linear ion trap mass spectrometer.

In a particularly preferred embodiment, the endophytes may be selected from the group consisting of E1, NEA10, NEA11, NEA12, NEA13, NEA14, NEA21, NEA23, NEA18, NEA19, NEA16 and NEA20.

In a particularly preferred embodiment, the endophyte variant may be selected from the group consisting of NEA12dh5, NEA12dh6, NEA12dh13, NEA12dh14, and NEA12dh17.

In a further aspect, the present invention provides a plant, plant seed or other plant part derived from a plant of the present invention and stably infected with an endophyte or endophyte variant of the present invention.

Preferably, the plant cell, plant, plant seed or other plant part is a grass, more preferably a forage, turf or bioenergy grass, such as those of the genera Lolium and Festuca, including L. perenne and L. arundinaceum.

By ‘plant cell’ is meant any self-propagating cell bounded by a semi-permeable membrane and containing plastid. Such a cell also required a cell wall if further propagation is desired. Plant cell, as used herein includes, without limitation, seeds suspension cultures, embryos, meristematic regions, callus tissue, leaves, roots, shoots, gametophytes, sporophytes, pollen and microspores.

In a further aspect, the present invention provides use of an endophyte or endophyte variant as hereinbefore described to produce a plant stably infected with said endophyte or endophyte variant.

In a still further aspect, the present invention provides a method of quantifying endophyte content of a plant, said method including measuring copies of a target sequence by quantitative PCR.

In a preferred embodiment, the method may be performed using an electronic device, such as a computer.

Preferably, quantitative PCR may be used to measure endophyte colonisation in planta, for example using a nucleic acid dye, such as SYBR Green chemistry, and qPCR-specific primer sets. The primer sets may be directed to a target sequence such as an endophyte gene, for example the peramine biosynthesis perA gene.

The development of a high-throughput PCR-based assay to measure endophyte biomass in planta may enable efficient screening of large numbers of plants to study endophyte-host plant biomass associations.

As used herein, except where the context requires otherwise, the term “comprise” and variations of the term, such as “comprising”, “comprises” and “comprised”, are not intended to exclude further additives, components, integers or steps.

Reference to any prior art in the specification is not, and should not be taken as, an acknowledgment or any form of suggestion that this prior art forms part of the common general knowledge in Australia or any other jurisdiction or that this prior art could reasonably be expected to be ascertained, understood and regarded as relevant by a person skilled in the art.

DETAILED DESCRIPTION OF THE EMBODIMENTS

In the figures:

FIG. 1 shows sequence alignment analysis of mating-type loci of endophyte strains E. festucae strain E2368, E1, NEA12 and ST. (SEQ ID Nos: 1-12)

FIG. 2A shows a UPGMA phenogram of genetic relationships among endophytes in ryegrass accessions of diverse origins and reference Neotyphodium and Epichloë species. Genetic identity was measured across 18 SSR loci using the Dice coefficient. Detailed annotations for sections A-D are shown in FIGS. 2B to 2E, respectively. Specifically, accessions analysed in this study are shaded in grey, the number of genotypes host to that endophyte strain from the total number of genotypes analysed are indicated in the round brackets and a representative host genotype is given in the square brackets. Endophyte isolates from the reference collection are specified in the square brackets following the species name. N. lolii Group 1 comprises of isolates Aries 1, Banks 5847, Ellett 5837, Fitzroy 2, Fitzroy 3, KT1-2, North African 6, Vedette 6645 and Victorian 2.

FIG. 3 shows isogenic inoculation methodology for endophyte inoculation. A. Meristem callus induction (4 weeks); B. Embryogenic callus proliferation (4 weeks); C. Shoot (and root) regeneration (5 days, 16 hours light); D. Endophyte inoculation; E. Plantlet growth (4 weeks, 16 hours light); F. Growth in soil (3 months); G. SSR-based analysis.

FIG. 4 shows the number of hits showing a given percent identity for 250 bp fragments of the NEA12 genome against the E. festucae and N. lolii genomes. The X-axis shows the percent identity, the Y-axis shows the number of hits. Black: N. lolii strain ST; White: E. festucae strain E2368.

FIG. 5 shows the number of hits showing a given percent identity for 250 bp segments of the E1 genome against the genomes of NEA12, E. festucae and N. lolii. The X-axis shows the percent identity, the Y-axis shows the number of hits. Black (1st bar in each group): E. festucae strain E2368; Grey (2nd bar in each group): Non-N. lolii strain NEA12; White (3rd bar in each group): N. lolii strain ST.

FIG. 6 shows the number of hits showing a given percent identity for 250 bp fragments of E1 against NEA12, E. festucae and N. lolii. The X-axis shows the percent identity, the Y-axis shows the number of hits expressed as a fraction of the total matches seen per comparison. Grey (1st bar in each group): E. festucae strain E2368; Black (2nd bar in each group): Non-N. lolii strain NEA12; White (3rd bar in each group): N. lolii strain ST.

FIG. 7 shows a schematic diagram of the mating-type loci in Neotyphodium/Epichloë.

FIG. 8 shows ClustalW analysis trees of the sequence flanking the mating-type loci (left), and the NoxR gene (cloned from E. festucae strain FL1 gi117413991; right).

FIG. 9 shows an alignment between mitochondrial genome of N. lolii strain Lp19 and a representative of the Clavicipitaceae, Metarhizium anisopliae (Genbank reference number NC_008068.1). While the two mitochondrial genomes vary in size, the genes are present in the same order and strand sense, with differences being due to variable insertions in the N. lolii mitochondrial genome.

FIG. 10 shows a depiction of part of the block structure of the mitochondrial genomes for each of the fungal endophytes sequenced in this study, as well as E. festucae strain E2368 and Metarhizium anisopliae for comparison. A shared block (e.g. b84) is present in all 12 mitochondria whereas block 85 is present only in the mitochondria of E. festucae strain E2368, and Non-N. lolii strains E1 and NEA12.

FIG. 11 shows a mitochondrial genome comparison. Parsimony tree of the relationships between the mitochondrial genomes of the 10 perennial ryegrass endophyte strains sequenced, E. festucae strain E2368 and Metarhizium anisopliae.

FIG. 12 shows a mitochondrial genome comparison. Neighbour joining tree analysis using ClustalW from a DNA alignment of the 40 blocks of sequence (˜40 kb) that are shared across the 10 perennial ryegrass endophyte strains sequenced, E. festucae strain E2368 and Metarhizium anisopliae.

FIG. 13 shows a standard curve for quantitative assessment of endophyte colonisation (copy number relative to total plant gDNA). (a) Tight clustering of amplification curves (4 technical replicates) ranging from 2×10² to 2×10⁶ copies of the 73 bp perA amplicon. (b) Dissociation curve analysis of the amplification curves shown in (a), with the presence of a single peak indicating primer pair specificity. (c) Assay performance is determined in terms of efficiency, precision and sensitivity. For a typical reaction, a slope of −3.1 to −3.6 and R² value≧0.985 is acceptable. This assay recorded a slope of −3.2 and R² value of 0.999.

FIG. 14 shows a quantitative assessment of endophyte colonisation in diverse ryegrass host panel. (a) Standard curve of perA target sequence (2×10² to 2×10⁶) and amplification curves of the unknown samples. (b) Dissociation curve analysis of the amplification curves shown in (a). (c) Standard curve for perA target (▪) and unknown samples (▴).

FIG. 15 shows a colchicine kill curve of endophyte strain ST mycelia grown in potato dextrose broth at 22° C., 150 rpm for 21 days.

FIG. 16 shows phenotype of colchicine treated colonies (0.1 and 0.2%) of endophyte strain ST compared to the untreated ST control. Mycelia were grown on potato dextrose agar at 22° C. in dark.

FIG. 17 shows an assessment for changes in ploidy level by flow cytometry. a) Dot plots and histogram overlay of control samples, ST, 13E9301 and NEA11. b) Dot plots and histogram overlay of two individual ST colonies (13 and 14), showing a shift in peak location relative to the controls.

FIG. 18 shows high throughput PCR screening method for detection of lolitrem B gene deletion mutants. The lolitrem genes targeted include: ItmM (480 bp), ItmJ (734 bp) and ItmC (583 bp). M: EasyLadder1 (100-2000 bp); 1-13: Individual putative lolitrem B gene deletion mutants; ST: ST DNA (positive control for ItmM, ItmJ and ItmC); AR1: AR1 DNA (positive control for ItmM and ItmC, negative control for ItmJ); H₂O PCR control.

FIG. 19 shows geographical origins represented in the tall fescue endophyte incidence assessment. This graph shows the 40 different geographic origins represented in the incidence assessment. The X axis gives geographic origins in the alphabetical order and the Y axis shows the number of accessions. The number of negative accessions is shown with black and the number of positive accessions is shown in grey.

FIG. 20 shows UPGMA phenogram of genetic relationships among endophytes in tall fescue accessions of diverse origins and reference Neotyphodium, Epichloë, FaTG-2 and FaTG-3 species.

FIG. 21 shows production of the insecticidal alkaloids loline, loline formate and peramine by tall fescue endophytes in their endogenous host.

FIG. 22 shows production of the anti-mammalian alkaloids ergovaline and lolitrem B by tall fescue endophytes in their endogenous host.

FIG. 23 shows an example of antifungal bioassay of inhibition reactions. Testing for antifungal activity of endophyte NEA12, ST and AR1 against 8 species of pathogenic fungi.

FIG. 24 shows endophytes selected for metabolic profiling in in vitro culture. Shown in the top left hand corner is the inhibition score.

FIG. 25 shows a method for sampling material for LCMS analysis.

FIG. 26 shows a validation assay. Rhizoctonia cerealis was grown in the presence of methanol extracts of endophyte mycelia. Shown is an example using the endophyte strain ST. A. Methanol extract of ST grown in the absence of R. cerealis; B. Methanol extract ST grown in presence of R. cerealis; C. Water only control; D. Methanol only control.

FIG. 27 shows structures of endophyte metabolites

1 peramine (MW 247.3); 2 ergovaline (MW 533.6); 3 lolitrem B (MW 685.9); 4 janthitrem I (MW 645.8); 5 janthitrem G (MW 629.8); 6 janthitrem F (MW 645.8).

FIG. 28 shows LCMS analysis of standard materials displaying extracted ion chromatogram for the toxins:

A. peramine

-   -   NL: 7.47E4     -   Base Peak m/z=47.50-248.50 F: ITMS+c ESI Full ms     -   [150.00-2000.00] MS         B. ergovaline     -   NL: 1.64E6     -   Base Peak m/z=533.40-534.40 F: ITMS+c ESI Full ms     -   [150.00-2000.00] MS         C. lolitrem B

NL: 2.25E3

Base Peak m/z=685.50-687.00 F: ITMS+c ESI Full ms

[150.00-2000.00] MS

FIG. 29 shows an LCMS comparison of AR37 inoculated perennial ryegrass with NEA12 inoculated perennial ryegrass (IMP04 NEA12 20).

A. AR37 no peramine

-   -   NL: 3.14E3     -   Base Peak m/z=247.50-248.50 F: ITMS+c ESI     -   Full ms [150.00-2000.00] MS         B. AR37 no ergovaline     -   NL: 7.39E4     -   Base Peak m/z=533.40-534.40 F: ITMS+c ESI     -   Full ms [150.00-2000.00] MS         C. AR37 no lolitrem B     -   NL: 1.32E4     -   Base Peak m/z=685.50-687.00 F: ITMS+c ESI     -   Full ms [150.00-2000.00] MS         D. AR37 janthitrem     -   NL: 8.68E4     -   Base Peak m/z=645.50-646.50 F: ITMS+c ESI     -   Full ms [150.00-2000.00] MS         E. NEA12 no peramine     -   NL: 6.18E3     -   Base Peak m/z=247.50-248.50 F: ITMS+c ESI     -   Full ms [150.00-2000.00] MS         F. NEA12 no ergovaline     -   NL: 4.10E3     -   Base Peak m/z=533.40-534.40 F: ITMS+c ESI     -   Full ms [150.00-2000.00] MS         G. NEA12 no lolitrem B     -   NL: 1.32E4     -   Base Peak m/z=685.50-687.00 F: ITMS+c ESI     -   Full ms [150.00-2000.00] MS         H. NEA12 janthitrem     -   NL: 1.04E4     -   Base Peak m/z=645.50-646.50 F: ITMS+c ESI     -   Full ms [150.00-2000.00] MS

FIG. 30 shows an MSMS analysis of NEA12 insulated perennial ryegrass metabolite 4. Inset is Table 2 from International patent application WO2004/106487 describing the fragmentations of the janthitrems found. Data for NEA12 metabolite 4 is in good agreement with that of component I in the table. (endo15June09-010 #3184 RT: 49.01 AV: 1 NL: 5.02E2, T: ITMS+cESId Full ms2 646.51@cid35.00 [165.00-660.00])

FIG. 31 shows Reverse phase liquid chromatography mass spectrometry (LCMS) analysis of A. TOLO3 NEA12 and B. TOLO3 ST. Profiles show the presence and absence of specific metabolites including peramine, ergovaline, lolitrem, and janthitrems.

FIG. 32 shows genotypic analysis of endophyte content in accessions from a targeted fescue germplasm collection.

FIG. 33 shows genetic diversity analysis of tall fescue endophytes.

FIG. 34 shows diversity analysis of host and endophyte.

FIG. 35 shows selection of fescue-endophyte combinations for metabolic profiling, endophyte isolation and isogenic inoculation.

FIG. 36 shows selection of fescue-endophyte combinations for metabolic profiling, endophyte isolation and isogenic inoculation.

FIG. 37 shows a desired toxin profile of tall fescue endophytes.

FIG. 38 shows a metabolic profile analysis.

FIG. 39 shows endophytes selected for semi-quantitative analysis of metabolites.

FIGS. 40 and 41 show metabolomics analyses of fescue endophytes.

FIG. 42 shows a semi-quantitative analysis of metabolic profile under temperature/water stress.

FIG. 43 shows endophytes selected for isogenic inoculation.

FIG. 44 shows SSR-based genotyping of isolated endophytes cultures prior to isogenic inoculation.

FIG. 45 shows endophyte vegetative stability in tall fescue and perennial ryegrass host genotypes (stability at 12 months post inoculation).

FIG. 46 shows endophytes selected for isogenic inoculation.

FIGS. 47-50 show metabolic profiling of isogenic tall fescue-endophyte associations.

FIG. 51 shows anti-fungal bioassays of fescue endophytes. Column 1 Colletotrichum graminicola, Column 2 Drechslera brizae, Column 3 Rhizoctonia cerealis.

FIG. 52 shows sequencing of selected novel fescue endophytes.

FIG. 53 shows peramine biosynthetic pathway.

FIGS. 54 A-C show presence of perA gene within non-Epichloe out-group endophytes (FIG. 54A NEA17; FIG. 54B NEA18; FIG. 54C NEA19).

FIG. 55 shows ergovaline biosynthetic pathway.

FIG. 56 shows genes in the eas gene cluster.

FIGS. 57 A-D show presence of dmaW gene for ergovaline biosynthesis in endophyte strains (FIG. 57A NEA17; FIG. 57B NEA16; FIG. 57C AR542; FIG. 57D NEA20).

FIGS. 58 A-D show presence of eas gene cluster for ergovaline biosynthesis. FIG. 58A FaTG-2 NEA17 (287819); FIG. 58B non-Epichloe out-group NEA18 (FEtc6-75); FIG. 58C FATG-3 NEA21 (231557); FIG. 58D N. coenophialum NEA16 (FEtc7-342).

FIG. 59 shows the Lolitrem B biosynthetic pathway.

FIG. 60 shows genes in the Lolitrem B biosynthetic gene cluster.

FIGS. 61 A-D show presence of Lolitrem B biosynthetic gene cluster 1 (ItmG, ItmM and ItmK) in endophyte strains. FIG. 61A FaTG-2 NEA17 (287819); FIG. 61B non-Epichloe out-group NEA18 (FEtc6-75); FIG. 61C FATG-3 NEA21 (231557); FIG. 61D N. coenophialum NEA16 (FEtc7-342).

FIGS. 62 A-D show presence of Lolitrem B biosynthetic gene cluster 2 (ItmB, ItmQ, ItmP, ItmF and ItmC) in endophyte strains. FIG. 62A FaTG-2 NEA17 (287819); FIG. 62B non-Epichloe out-group NEA18 (FEtc6-75); FIG. 62C FATG-3 NEA21 (231557); FIG. 62D N. coenophialum NEA16 (FEtc7-342).

FIGS. 63 A-D show presence of Lolitrem B biosynthetic gene cluster 3 (ItmE and ItmJ) in endophyte strains. FIG. 63A FaTG-2 NEA17 (287819); FIG. 63B non-Epichloe out-group NEA18 (FEtc6-75); FIG. 63C FATG-3 NEA21 (231557); FIG. 63D N. coenophialum NEA16 (FEtc7-342).

FIG. 64 shows the loline biosynthetic pathway.

FIG. 65 shows the loline biosynthetic gene cluster.

FIGS. 66 A-D show presence of Loline biosynthetic gene cluster in endophyte strains. FIG. 66A FaTG-2 NEA17 (287819); FIG. 66B non-Epichloe out-group NEA18 (FEtc6-75); FIG. 66C FATG-3 NEA21 (231557); FIG. 66D N. coenophialum NEA16 (FEtc7-342).

FIGS. 67 A-F show alkaloid biosynthetic gene analysis for endophyte strain NEA23 (269850). FIG. 67A Presence of loline gene cluster; FIG. 67B Presence of peramine gene; FIG. 67C Analysis of Lolitrem gene cluster 01; FIG. 67D Analysis of Lolitrem gene clusters 02 and 03; FIG. 67E Analysis of dmaW gene for ergovaline production; FIG. 67F Analysis of eas gene cluster for ergovaline production.

FIG. 68 shows genotypic analysis of NEA23 and NEA21.

FIG. 69 shows genotypic analysis of NEA16 and NEA20.

FIG. 70 shows the structures of Lolitrem B, Erogvaline and Peramine, with desirable toxin profiles indicated.

FIG. 71 shows in vitro bioassays to assess antifungal activity of Neotyphodium endophytes.

FIG. 72 shows a detached leaf assay to assess resistance to crown rust (Puccinia coronata f. sp. Lolii) of perennial ryegrass plants with and without Neotyphodium endophytes.

FIG. 73 shows glasshouse and field trial screens for drought tolerance and water use efficiency of perennial ryegrass plants with and without Neotyphodium endophytes.

FIG. 74 shows the steps involved in cell division.

FIG. 75 shows experimental work flow for chromosome doubling of endophyte cells.

FIG. 76 shows flow cytometry calibrations for DNA content assessment in Neotyphodium endophyte strains. Peaks indicate relative nuclear DNA content.

FIG. 77 shows flow cytometry analysis of NEA12^(dh) Neotyphodium endophyte strains.

FIG. 78 shows analysis of growth rate in culture after 8 weeks of NEA12^(dh) Neotyphodium endophyte strains compared to control endophyte strains.

FIG. 79 shows analysis of growth rate in culture over 5 weeks of NEA12^(dh) Neotyphodium endophyte strains compared to control endophyte strains.

FIG. 80 shows antifungal bioassays of NEA12^(dh) Neotyphodium endophyte strains.

FIG. 81 shows antifungal bioassays of NEA12^(dh) Neotyphodium endophyte strains.

FIG. 82 shows analysis of genome survey sequencing read depth of colchicine-treated Neotyphodium endophyte strains.

FIG. 83 shows analysis of genome survey sequencing reads mapping to NEA12 genome survey sequence assembly.

FIG. 84 shows experimental work flow for X-ray mutagenesis.

FIG. 85 shows the indole-diterpene biosynthetic pathway of Neotyphodium endophytes.

FIG. 86 shows in vitro growth of X-ray irradiated Neotyphodium endophyte strains.

FIG. 87 shows Itm gene clusters of Neotyphodium endophytes.

FIG. 88 shows determination of genome sequence variation in X-ray irradiated Neotyphodium endophyte strains.

FIG. 89 shows single nucleotide polymorphisms (SNPs) in genome sequences of X-ray irradiated Neotyphodium endophyte strains. (SEQ ID Nos. 22-47)

FIG. 90 shows small insertions/deletions (INDELs) in genome sequences of X-ray irradiated Neotyphodium endophyte strains. (SEQ ID Nos.48-85)

FIG. 91 shows deletions in genome sequences of X-ray irradiated Neotyphodium endophyte strains.

FIG. 92 shows numbers of SNPs in genic regions of genome sequences of X-ray irradiated Neotyphodium endophyte strains.

FIG. 93 shows numbers of INDELs in genic regions of genome sequences of X-ray irradiated Neotyphodium endophyte strains.

FIG. 94 shows the spectrum of genome sequence changes (deletions) in genome sequences of X-ray irradiated Neotyphodium endophyte strains.

FIG. 95 shows mutagenesis index of X-ray irradiated strains based on number of genome sequence changes observed in genome sequences of X-ray irradiated Neotyphodium endophyte strains.

FIG. 96 shows metabolic profiling of NEA12^(dh) Neotyphodium endophyte strains.

FIG. 97 shows metabolic profiling of X-ray irradiated Neotyphodium endophyte strains.

EXAMPLE 1—IDENTIFICATION OF NOVEL ENDOPHYTES

A collection of 244 perennial grass accessions was assembled for the discovery of novel endophyte strains. The collection targeted accessions from the Northern Mediterranean and Eastern Europe for endophytes that lack lolitrems, as well as accessions from the Middle East, the proposed centre of origin of perennial ryegrass and N. lolii.

Genotypic analysis of endophyte content was performed across a total of 189 accessions. From each accession 1-5 plant genotypes were analysed for endophyte. Endophyte incidence was low, with endophyte detected in 51% of accessions. Endophyte was consistently detected (with 0 SSR markers) in 77 of the accessions.

Endophytes representing five different taxa were detected across the 77 accessions with 18 SSR markers used to investigate endophyte diversity in perennial ryegrass (FIG. 2). N. lolii was predominant, occurring in 63 accessions. Also detected, although less common, were LpTG-2 and putatively new taxa.

Genetic variation in N. lolii appeared to be low. A total of 22 unique genotypes were detected across the 63 accessions host to N. lolii.

The likely toxin profiles of 14 of the 22 genotypes were established from comparisons with genetic and phenotypic data from previous studies. Most of these genotypes (12/14) showed genetic similarity to endophytes known to produce lolitrems.

There were two genotypes that showed genetic similarity to genotypes known to lack lolitrems but produce ergovaline. One of these genotypes was identical to the genotype detected in the endophyte NEA6. The likely toxin profiles of the remaining eight genotypes were not known. These genotypes did not show high levels of genetic similarity to the endophytes AR1, Endosafe, NEA3 or NEA5.

Plants carrying candidate endophytes were subjected to primary metabolic profiling in the endogenous genetic background, through clonal propagation and measurement of toxin levels. A total of 42 genotypes representing four of the five taxa were selected for toxin profiling, including the eight novel genotypes with unknown toxin profiles. The perennial ryegrass genotype North African 6 (NA₆), which contains standard toxic (ST) endophyte, was used as a control.

For metabolic profiling, a complete randomised block design was used, with four replicate clones for each plant and using four hydroponics tubs as blocks. Following three months in hydroponics, whole shoot (leaf plus basal region) was harvested from each plant. The fresh and dry weights of each plant were measured and powdered sample material from 80 (20 genotypes×4 replicates) samples (three tillers per sample) analysed for alkaloid content (lolitrem, ergovaline and peramine).

EXAMPLE 2—CANDIDATE ENDOPHYTES

Candidate endophytes for further study were chosen on the basis of their genetic identity and metabolic profile. Host-endophyte combinations producing significant amounts of lolitrem B were eliminated, as the ryegrass staggers syndrome produced by this alkaloid is the most important limitation for livestock production.

The candidate endophyte NEA10 (originating from Spain) was identified as a novel genotype in this analysis with an unknown toxin profile. Its genetic identity is a unique N. lolii strain. Following in planta metabolic profiling analysis, candidate endophyte NEA10 was found to produce ergovaline and peramine, and not lolitrem B.

The candidate endophyte NEA11 (originating from France) was identified as a novel genotype in this analysis with an unknown toxin profile. Its genetic identity is a unique LpTG-2 strain. Following in planta metabolic profiling analysis, candidate endophyte NEA11 was found to produce ergovaline and peramine, and not lolitrem B.

The candidate endophyte NEA12 (originating from France) was identified as a novel genotype in this analysis with an unknown toxin profile. NEA12 is a genetically novel, non-Neotyphodium lolii, endophyte representative of an as yet un-named taxon. Following in planta metabolic profiling analysis, candidate endophyte NEA12 was found to not produce the three alkaloids assessed (lolitrem B, ergovaline and peramine).

The candidate endophyte E1 was identified as a novel genotype in this analysis with an unknown toxin profile. E1 is a genetically novel, non-Neotyphodiumlolii, endophyte representative of an as yet un-named taxon. Following in planta metabolic profiling analysis, candidate endophyte E1 was found to not produce the three alkaloids assessed (lolitrem B, ergovaline and peramine).

EXAMPLE 3—METHODOLOGIES FOR ENDOPHYTE CHARACTERISATION Endophyte Isolation

Novel candidate endophytes were isolated from their host plant to establish an in vitro culture. Following isolation, the genotype of each endophyte was confirmed by SSR analysis to ensure a high level of quality control prior to inception of isogenic inoculations.

Establishment of Meristem Cultures for a Diverse Perennial Ryegrass Host Panel

A set of cultivars representing elite germplasm were obtained, including forage and turf types. Meristem cultures from different cultivars were established to evaluate and compare the phenotypic properties of novel endophyte strains in diverse isogenic host backgrounds. Embryogenic genotypes were identified for each of the cultivars through callus induction and proliferation. Subsequent regeneration of embryogenic genotypes identified primary tissue culture responsive (pTCR) genotypes for each of the cultivars. The number of pTCR genotypes with regeneration frequencies ranging from 80-100% varied from 1-4 per cultivar. pTCR genotypes were then prepared for meristem-derived callus induction to identify highly regenerable genotypes for isogeneic endophyte inoculation. Table 1 shows a selection of cultivars developed, and the tissue culture responsive (TCR) genotype, used for isogenic inoculation.

TABLE 1 Summary information for perennial cultivars selected for isogenic inoculation. TCR genotype used Cultivar Characteristics for inoculation Bealey Tetraploid forage type Bea 02 Bronsyn Standard forage type with robust Bro 08 endophyte performance Impact Late flowering, dense tillering Imp 04 forage type Barsandra Turf type San 02 Tolosa Distinct forage type Tol 03

Isogenic Inoculation of Novel Perennial Ryegrass Endophytes

In order to accurately determine the phenotypic effects of different candidate endophytes in the absence of host-specific genetic effects, a system for isogenic inoculation was developed (FIG. 3). The regenerating callus method of inoculation was chosen, as it results in a relatively high rate of inoculation compared to other tested techniques, and the achieved isogenic inoculation rate was similar to the standard inoculation procedure for non-isogenic seedlings. Novel candidate endophytes NEA10, NEA11, NEA12, E1 and control endophyte ST were individually inoculated into elite germplasm. The logistical approach was to inoculate two cultivars at any given time, with one TCR genotype for each variety chosen for inoculation in this initial study. For each cultivar-endophyte combination, 30 replicate inoculations were performed, 25 of these replicates being transferred to soil. Following inoculation and plantlet regeneration in culture, plants were transferred to soil for three months to allow establishment of endophyte and host-plant associations. After this period, three tillers from each plant were sampled and tested for endophyte presence using SSR-based analysis.

A quantitative score was used to assess endophyte inoculation frequency (Table 2). Three diagnostic SSR markers were used to determine endophyte presence and identity and samples were scored on a scale of 0-3.

Of the 570 inoculations tested, 195 (34.2%) could be positively scored with a high degree of confidence (Table 3). Successful inoculations are listed on Table 3.

TABLE 2 SSR screening for endophyte presence in planta. Quantitative Alleles present and of correct score size for given SSR loci 3 Endophyte present 2 Endophyte present 1 Endophyte absent 0 Endophyte absent

TABLE 3 Summary statistics for isogenic inoculation of selected candidate endophytes into a targeted perennial ryegrass panel of 5 hosts. NEA10 NEA11 NEA12 E1 ST Total A. Number of positive inoculants Bea02 0 12 3 4 8 27 Bro08 0 14 1 13 13 41 Imp04 3 40 4 10 16 73 San02 0 17 6 6 11 40 Tol03 0 3 2 6 3 14 Total 3 86 16 39 51 195 B. Total number of inoculations tested Bea02 24 18 20 19 25 106 Bro08 19 15 20 18 25 97 Imp04 31 49 21 12 35 148 San02 47 39 24 7 32 149 Tol03 17 7 18 17 11 70 Total 138 128 103 73 128 570 C. Percent of positive inoculants Bea02 0.0 66.7 15.0 21.1 32.0 25.5 Bro08 0.0 93.3 5.0 72.2 52.0 42.3 Imp04 9.7 81.6 19.0 83.3 45.7 49.3 San02 0.0 43.6 25.0 85.7 34.4 26.8 Tol03 0.0 42.9 11.1 35.3 27.3 20.0 Average 2.2 67.2 15.5 53.4 39.8 34.2

Variation in inoculation success according to candidate endophyte identity was observed (Table 3). Endophyte NEA10 (2.2%), for example, exhibited relatively lower success rates as compared to NEA11 (67.2%), or the commercial endophyte ST (39.8%; Table 4) and only formed stable associations with one of the five hosts in the panel (Impact). Endophyte E1 is a highly compatible endophyte, which obtained a high rate of success of inoculation into perennial ryegrass (Table 3) compared to other endophytes examined, including the strain ST.

Variation was also observed between host plant genotypes for successful inoculations (Table 3). Tolosa (20.0%) appears to be more recalcitrant to inoculation compared to host plants such as Bronsyn (42.3%) and Impact (49.3%).

Vegetative Stability of Isogenic Perennial Ryegrass-Fungal Endophyte Associations

Fully confirmed endophyte positive plants from the targeted host-endophyte panel (host plants Bealey, Bronsyn, Barsandra, Tolosa and Impact; endophytes ST, NEA10, NEA11, NEA12) were retested 6-12 months after inoculation and 18-24 months after inoculation, to confirm the presence of endophyte and to assess vegetative stability. In this experiment, 3 replicates of 3 tillers each (total of 9 tillers) were collected for SSR-based analysis.

Most of the previously confirmed endophyte positive plants were again confirmed in this study at 6-12 months post inoculation, indicating that each of the host-endophyte combinations were stable (Table 4). Endophyte NEA12 appears to be less stable in planta, as 7 of the 13 previously confirmed samples could not be fully confirmed in this experiment (Table 4). ST also showed lower levels of stability compared to NEA11, with 7/21 samples not re-confirmed in this study (Table 4). Following this analysis, up to three independent inoculation events from each host plant-endophyte combination were retained for further study.

At 18-24 months post inoculation, plants were further assessed for long term vegetative stability (Table 4). ST, NEA10 and NEA11 each exhibit stable associations, with most plants retaining endophyte. NEA12 appears to be less stable in some associations, however does form stable long term associations with Tolosa.

TABLE 4 Endophyte frequency in priority ryegrass host panel genotypes in re- sampled plants that were previously fully confirmed. Plants were re- sampled 6-12 months (shown in bold text) post inoculation and again after 18-24 months post inoculation (shown in normal text). Plant Endophyte genotype genotype ST NEA10 NEA11 NEA12 Impact  9/10 2/3 12/12 1/4 (Imp04) 3/3 2/2 3/3 1/1 Barsandra 4/6 7/7 2/4 (San02) 2/3 NA 3/3 1/2 Tolosa 1/2 3/3 2/2 (Tol03) 1/1 NA 2/3 2/2 Bealey 3/3 9/9 0/2 (Bea02) 2/3 NA 3/3 0/1 Bronsyn 3/6 9/9 1/1 (Bro08) 2/2 NA 4/4 0/1 NA = not applicable, as no fully confirmed plants were previously identified.

Metabolic Profiling of Isogenic Perennial Ryegrass-Fungal Endophyte Associations

Metabolic profiling was conducted to determine the stability of the predicted endophyte phenotype in a range of different host genotype backgrounds. Four replicates of three tillers each were grown under optimal conditions in hydroponics for six weeks prior to measuring lolitrem B, ergovaline and peramine levels. Each replicate plant was also tested for the presence/identity of endophyte using SSR-based genotyping in order to correlate toxin profile with endophyte presence, in particular for those instances were toxin profiles were negative for the alkaloids measured.

Table 5 summarises the outcomes of metabolic profiling in hydroponics for both the endophyte discovery phase and the isogenic inoculation phase. Toxin profiles were as predicted from the cluster assignment of the endophyte in the diversity analysis and the toxin profiles measured in the endogenous host plant.

TABLE 5 Metabolic profile of candidate endophytes. Endophyte Endogenous Isogenic strain toxin profile toxin profile^(b) Origin Species NEA10 —/E/n.d^(a)/— —/E/P/— Spain N. lolii NEA11 —/E/n.d/— —/E/P/— France LpTG-2 NEA12 —/—/—/n.d —/—/—/J France non-N. lolii E1 n.d —/—/—/— non-N. lolii ST L/E/P/— L/E/P/— N. lolii Toxins are listed in order: L = Lolitrem B; E = Ergovaline; P = Peramine; J = Janthitrems ^(a)Peramine not measured in NEA10 and NEA11 samples; Janthitrems not measured in NEA12 samples ^(b)Toxin profile in isogenic associations

Genome Survey Sequencing of Candidate Fungal Endophytes Nuclear Genome Assembly

Genome Survey Sequencing was performed for non-N. lolii strains NEA12 and E1, LpTG-2 strain NEA11 and Neotyphodium lolii strains including Standard Toxic (ST) and NEA10 using GSFLX Titanium (TI-GSFLX) pyrosequencing technology (Roche; as per manufacturers instructions). A further five N. lolii strains were sequenced using either GSFLX Standard or GS20 pyrosequencing technology. Genome assembly for each of the strains was conducted with GSFLX De Novo Assembler (Table 6).

A new genome assembly was performed for N. lolii strain ST (GSFLX De Novo Assembler), combining sequence reads from both GSFLX and TI-GSFLX runs. Table 7 compares the assembly of single and multiple strains. This combined assembly of the ST genome achieves c.12× coverage of the c.32 Mbp haploid genome. The genome is assembled into 7,875 large contigs (0.5 to 47 kb) of which the net length is 31,750,111 bp.

Analysis using Augustus gene prediction software trained for Fusarium graminearum shows that there are 11,517 predicted protein coding genes in the N. lolii genome.

TABLE 6 Summary statistics for GS-FLX based whole genome sequencing of candidate endophytes. N. lolii N. lolii N. lolii N. lolii N. lolii N. lolii Lp19 ST NEA3 AR1 E9 G4 Genome size (Mb) ~29 ~29 ~29 ~29 ~29 ~29 Toxin profile^(a) L + E + P L + E + P E + P P L + P L + P 454 Sequencer GS20 GSFLX GSFLX GSFLX GSFLX GSFLX Standard Standard Standard Standard Standard Number of sequencing runs 1 1 1 1 1 1½ Number of high quality reads 449,408 288,527 361,154 437,465 344,074 631,248 Number of bases in high quality reads 47,820,858 71,810,513 84,032,924 97,510,674 85,419,382 146,574,403 Average read length (bases) 106 249 232 223 249 215 Origin of reads assembled^(b) nuclear + nuclear + nuclear + nuclear + mt nuclear + mt nuclear + mt mt mt mt Large contigs (>500 bases) Number of contigs 6 2,524 5,251 6,070 6,612 12,663 number of bases 99,508 1,834,624 3,911,733 4,650,113 5,208,116 12,393,467 average contig size 16,584 726 744 766 787 978 N50 contig size 88,709 680 723 751 774 1039 largest contig size (bases) 88,709 65,108 15,473 19,024 81,839 29,071 All contigs number of contigs 29,013 28,137 33,262 33,777 33,136 32,796 number of bases 3,532,954 7,999,326 10,842,510 11,755,707 12,022,601 17,790,671 N. lolii N. lolii non-N. lolii non-N. lolii LpTG-2 NEA10 ST E1 NEA12 NEA11 Genome size (Mb) ~29 ~28 TBD TBD ~55 Toxin profile^(a) E + P L + E + P TBD J E + P 454 Sequencer GSFLX GSFLX GSFLX GSFLX GSFLX Titanium Titanium Titanium Titanium Titanium Number of sequencing runs ½ 1 ½ ½ ½ Number of high quality reads 580,060 1,220,036 539,019 399,868 456,111 Number of bases in high quality reads 221,859,987 451,459,919 202,854,865 165,826,144 177,307,015 Average read length (bases) 383 370 377 415 389 Origin of reads assembled^(b) nuclear + mt nuclear nuclear + nuclear + nuclear + mt mt mt Large contigs (>500 bases) Number of contigs 7,272 4,198 9,139 12,399 14,791 number of bases 26,931,240 24,382,151 27,150,736 17,300,350 16,306,033 average contig size 3703 5,808 2970 1,395 1,102 N50 contig size 7668 11,026 5845 1,703 1,214 largest contig size (bases) 50,291 90,675 40,456 16,319 59,986 All contigs number of contigs 11,809 6,962 15,589 20,640 39,791 number of bases 28,155,780 25,104,969 28,916,589 19,862,340 23,307,237 ^(a)L = Lolitrem B, E = Ergovaline, P = Peramine, J = Janthitrems ^(b)Newbler Assembler

TABLE 7 Assembly comparison of single and multiple strains of N. lolii endophyte Lp19 ST NEA3 AR1 E9 G4 454 Sequencer GS 20 GS FLX GS FLX GS FLX GS FLX GS FLX (Standard) (Standard) (Standard) (Standard) (Standard) Number of sequencing runs 1   1^(a) 1 1   1^(a)   1^(b) Number of reads 282,604 191,848  257,381 311,444 267,445  446,017  Number of bases in reads 28,628,965 46,613,713    58,666,512 68,947,121 65,192,155    101,770,051     Large contigs (≧500 bases) number of contigs 109 1,419 3,210 3,519 4,560 11,895  number of bases 124,393 909,187  2,111,227 2,317,893 3,041,084    9,249,140    average contig size 1,141   640 657 658   666   777 N50 contig size^(c) 1,193   606 632 636   644   774 largest contig size (bases) 7,867 8,639 7,382 8,816 8,016 8,226 Q40 plus bases (%)^(d) 90.62    93.97 93.43 93.90    93.72    94.64 All contigs (≧100 bases) number of contigs 2,183 8,769 12,434 15,324 15,126  28,456  number of bases 500,187 2,911,985    4,778,407 5,584,622 6,123,678    14,307,808    ST combined ST ST + NEA3 + AR1 + E9 + G4 454 Sequencer GS FLX GS FLX GS FLX (Titanium) (Standard + Titanium) (Standard) Number of sequencing runs 1 2 5 Number of reads 913,566 1,105,414 1,474,135 Number of bases in reads 334,946,727 381,560,440 341,189,552 Large contigs (≧500 bases) number of contigs 8,825 7,875 11,905 number of bases 31,669,111 31,750,111 26,515,831 average contig size 3,588 4,031 2,227 N50 contig size^(c) 6,142 7,231 3,435 largest contig size (bases) 46,664 46,668 24,527 Q40 plus bases (%)^(d) 98.03 98.52 98.32 All contigs (≧100 bases) number of contigs 11,324 10,555 21,836 number of bases 32,350,205 32,482,543 29,165,397

Alkaloid Biosynthetic Gene Content

The content of genes known to be involved in alkaloid production in each of the sequenced endophyte genomes was investigated. Sequence reads for each of the strains were subjected to a BLAST(N) search against each of the known toxin gene sequences (downloaded from NCBI) to determine the degree of gene coverage by sequence reads. Table 8 below shows the correlation between secondary metabolite production and toxin-related gene content in endophyte genomes.

Based on this analysis, endophyte strain E1 is predicted to produce the alkaloids peramine and ergovaline, but not loline or lolitrem B. In planta analysis of alkaloid content has shown that E1 does indeed not produce loline or lolitrem B.

NEA10 and NEA11 produce ergovaline and peramine, but not lolitrem B. The NEA11 sequence provides evidence for 2 peramine biosynthesis genes, as might be expected in a heteroploid genome.

NEA12, known to lack production of ergot alkaloids and lolitrem B, also lacks corresponding biosynthetic genes.

Nuclear Genome Comparison

Comparison of the NEA12 Nuclear Genome to E. festucae E2368 and N. Lolii ST

To compare the nuclear genome of NEA12 to E. festucae and N. lolii, the contigs derived from NEA12 were split into 250 bp segments and these segments were used as BLAST(N) queries against E. festucae strain E2368 (University of Kentucky, http://www.genome.ou.edu.fungi.html) and N. lolii ST contigs. One hit was scored for each 250 bp contig if it was greater than 50 bp long and greater than 80% identity. Summary statistics were taken for NEA12 250 bp fragments against E. festucae and N. lolii (FIG. 4).

The number of hits showing a given percent identity shows there are more 250 bp segments that give 100 percent identity matches against an E. festucae genome than a N. lolii genome.

The above statistic is independent of the length of the overlap. An identical 250 bp region would give a 250 bp overlap with a percent identity of 100. The number and proportion of these identical reads is given for the two searches below (Table 9).

TABLE 9 The number and proportion of identical reads between NEA12 and an E. festucae genome and a N. lolii genome. ST E. festucae Total Number of identical reads 16914 28866 89416 (100% identity between 250 bp segment) Percent of identical reads 18.92 32.28 (100% identity between 250 bp segment)

There are also segments that have no match to either N. lolii (6051) or E. festucae (5670). These data suggest that NEA12 is a new endophyte taxon that is genetically closer to E. festucae than N. lolii. This data supports the earlier observation, using SSR-based genetic diversity analysis, that NEA12 is genetically distinct from N. lolii and E. festucae.

Comparison of E1 Nuclear Genome to NEA12, E. Festucae E2368 and N. lolii ST

For comparison at the whole genome level, the contigs from endophyte strain E1 were split into 123,258 250 bp segments. Each 250 bp segment was used as a BLAST(N) query against the assembled whole genome DNA sequences from NEA12, E. festucae E2368 and N. lolii ST (FIG. 5). A BLAST(N) hit was recorded if there was an overlap of greater than 49 bp. The number of overlaps at a given percent identity was counted for each search. The plot of this data reveals that the genome of endophyte strain E1 is more similar to that of E. festucae strain E2368 than to either N. lolii strain ST or NEA12.

The assembled contigs from NEA12 sum to c.17.3 Mb, so the level of sequence similarity to that endophyte is probably underestimated due to limited scope for comparison. If the similarity is expressed as a fraction of the total matches observed per comparison, strain E1 is seen to be more similar to strain NEA12 than to N. lolii strain ST (FIG. 6). The property of enhance similarity between E1 and E. festucae as compared to N. lolii is similar to the pattern seen with mitochondrial genome analysis.

LpTG-2 Endophyte NEA11

The LpTG-2 endophyte strain NEA11 is reported to be a hybrid of N. lolii and E. typhina. Mitochondrial sequence analysis supports the hybridisation of E. typhina with a N. lolii with only the N. lolii mitochondria being retained.

Evidence for the hybrid nuclear genome is seen when nuclear genes are used as a query against contigs from the NEA11 genome assembly (FIGS. 7 and 8).

The panels below show a region of the ‘UDP-N-acetylglucosaminyltransferase’ gene from E. festucae being used as a BLAST(N) query against: E. festucae (E2368) genome contigs; N. lolii (ST) genome contigs; and LpTG-2 (NEA11) genome contigs. This result clearly shows a second variant of this gene in the NEA11 genome that has far more SNPs than the first NEA11 contig hit. This presumably represents the E. typhina copy of this gene that has been retained in the NEA11 genome. It is unlikely that this is a localised duplication in NEA11 as neither E. festucae, nor N. lolii has such a duplication.

1: E. festucae (E2368) genome contigs (SEQ ID NO: 13)

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2. N. lolii (ST) genome contigs (SEQ ID NO: 14)

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3. LpTG-2 (NEA11) genome contigs (SEQ ID NO: 15)

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211

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151

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 91

  1

indicates data missing or illegible when filed

The panel below shows the N. lolii peramine gene from GenBank used as a query against NEA11 genome assembly contigs. BLAST(N) alignment of LpTG-2 endophyte strain NEA11 reads against the peramine gene (perA) sequence (GenBank accession number: AB205145). (SEQ ID Nos: 16-21) The presence of SNP in one set of contigs indicates the presence of two copies of the peramine gene sequence in endophyte strain NEA11.

1536 gcgcgtcacgatttcccatttaacaccctcagtcacgcggctgatagacccagattcaca

  24 ............................................................ 83

  24 ............................................................ 83

 450 ...... 455

 247 .............g.........................a.................... 306

 247 .............g.........................a.................... 306

 247 .............g.........................a.................... 306

 52 .............g.........................a.................... 1

.............g.........................a.................... 310

1656 accttttctaaagacgatggtgtttaccggcgagcctctgtctgtggacgatgctacccg 1715

  84 ............................................................ 143

  84 ............................................................ 143

 307 ...cg.c..c.................................................. 366

 307 ...cg.c..c.................................................. 366

 307 ...cg.c..c.................................................. 366

 311 ...cg.c..c............... 335

1775 atggtggggaaaggtcgacgtcgtcaacgaatatgggcctgcagagtgcaccatcaacac 1775

 144 ............................................................ 203

 144 ............................................................ 203

 367 ............................................................ 426

 367 ............................................................ 426

 367 ............................................................ 426

1776 tgtcaacagccgacctatcagtcctgaagctgctacgaacatagggctgccggttggagt

204 ............................................................ 263

204 ............................................................ 263

427 ..............................c...g......................... 486

427 ..............................c...g......................... 486

427 ..............................c...g......................... 486

1836 ggccgcttggattaccgacccggaaaaccatcaagtactcgttccgatcggctgtgttgg

264 ............................................................ 323

264 ............................................................ 323

487 ...............a........... 513

487 ...............a........... 513

487 ...............

4                 ...........tg................a..............

indicates data missing or illegible when filed

Mating-Type Analysis

In heterothallic fungi, such as Epichloë spp, strains must be of opposite mating-type for sexual reproduction to proceed. In Epichloë spp, sexual development is regulated by alternative MAT1-1 (comprising MAT1-1-1, MAT1-1-2 and MAT1-1-3) and MAT1-2 (comprising MAT1-2-1) genes at the MAT locus. Although the flanking regions of MAT1-1 and MAT1-2 are homologous, the nucleotide sequences of MAT1-1 and MAT1-2 idiomorphs are highly dissimilar (FIG. 7).

The mating-type locus of E. festucae E2368 was contained in contig 5 of the original assembly (University of Kentucky, http://www.genome.ou.edu.fungi.html). This contig was aligned with contigs derived from N. lolii endophyte strain ST. The MAT1-1 mating-type locus genes found in E. festucae (MAT1-1-1, MAT1-1-2, MAT1-1-3) were demonstrated to be absent in the N. lolii consensus sequence (FIG. 7). In the corresponding location a single gene for the opposite mating type (MAT1-2) was identified. This opposite mating type gene (MAT1-2-1) was found in all the N. lolii strains sequenced as well as NEA12 (Table 10).

To assess the mating type of endophyte strain E1, the two possible mating type contigs were compared to E1 contigs. This activity proved that E1 contained the same three (MAT1-1-1, MAT1-1-2, MAT1-1-3) mating-type genes as E. festucae E2368 and is thus of the MAT1-1 mating-type. This is in contrast to the mating type gene of non-N. lolii strain NEA12, which is of the MAT1-2, N. lolii-like, mating-type.

Cluster analysis based on sequence nucleotide diversity shows that endophyte strains E1 and NEA12 cluster with E. festucae strain E2368, with their position in the tree switching between analysis based on the mating-type loci flanking sequence and the NoxR gene respectively, and suggesting that recombination has occurred in these lineages (FIG. 8).

The identification of an endophyte strain of the opposite mating-type to previously characterised perennial ryegrass endophyte strains provides a means for molecular breeding of endophytes to deliver favourable traits into the plant endophyte symbiotum through the use of the novel E1 strain endophyte.

Mitochondrial Genome Analysis

The mitochondrial genome of N. lolii endophyte strain Lp19 was present as a single c.88.7 kb contig. This sequence was used to identify contigs containing mitochondrial DNA sequences in the other N. lolii strains sequenced through BLAST(N)-based sequence similarity. Homology searches identified mitochondrial contigs in the E. festucae strain E2368 assembly the two non-N. lolii genomes and the LpTG-2 genome that were sequenced.

The mitochondrial genome sizes for each of the fungal endophytes sequenced in this study as well as the E. festucae strain E2368 are shown on Table 11. A representative of the Clavicipitaceae, Metarhizium anisopliae (Genbank reference number NC_008068.1), is shown for comparison. The N. lolii mitochondrial genomes are similar in size, ranging from 88,377 bp for G4 to 88,740 bp for AR1. LpTG-2 representative, NEA11 has a mitochondrion genome similar in size to N. lolii. The two non-N. lolii genomes, E1 (63,218 bp) and NEA12 (57,818 bp), have relatively smaller mitochondrial genomes more similar in size to that of E. festucae strain E2368 (69,614 bp) than that of N. lolii.

TABLE 11 Mitochondrial genome size of the 10 fungal endophyte strains sequenced in this study, E. festucae strain E2368 and Metarhizium anisopliae. non- non- Epichlo{umlaut over (e)} N. lolii N. lolii N. lolii N. lolii N. lolii N. lolii N. lolii N. lolii N. lolii LpTG-2 festucae Metarhizium Lp19 ST NEA3 AR1 E9 G4 NEA10 E1 NEA12 NEA11 2368 anisopliae Approximate Mitochondrial 88709 88711 87526 88740 88738 88377 88734 63219 57818 88692 69614 24674 Genome Lengths (bp)

The multiple mitochondrial DNA sequences were used to generate a mitochondrial genome alignment along with the mitochondrial genome sequence of the Clavicipitaceae fungus Metarhizium anisopliae. The alignment demonstrated that while the different mitochondrial genomes vary in size, the genes are present in the same order and strand sense in all genomes, with differences being due to variable insertions in each strain (FIGS. 9 and 10).

Scoring block presence as 1 and absence as 0, a matrix was created to generate a parsimony tree of the relationships between the mitochondrial genomes (FIG. 11). This tree places the E1 and NEA12 mitochondria on a branch with the E. festucae strain E2368 mitochondrial genome, these three genomes showing greater variation than that of the N. lolii mitochondria. The mitochondrial tree shows that endophyte strains NEA12 and E1 are neither E. festucae nor N. lolii, but are more similar to E. festucae than N. lolii. Endophyte LpTG-2 NEA11 has a mitochondrial genome that is genetically a N. lolii type, being in a clade with NEA3 and AR1, within the N. lolii cluster.

A similar pattern is observed if a neighbour joining tree is constructed using ClustalW from a DNA alignment of only the 40 blocks of sequence that are shared across all endophyte species (c. 40 kb; FIG. 12). There are still gaps present in the Metarhizium anisopliae sequence in this alignment.

A Quantitative PCR Method for Assaying Endophyte Biomass in Planta

A quantitative PCR (qPCR) method for assaying endophyte biomass in planta has been developed and successfully implemented. The development of a high-throughput PCR-based assay to measure endophyte biomass in planta enables efficient screening of large numbers of plants to study endophyte-ryegrass biomass associations. qPCR-specific primer sets have been designed for the peramine biosynthesis gene (perA). To quantitatively assess in planta endophyte biomass, a standard curve, ranging from 2×10² to 2×10⁶ copies of the target sequence, has been generated from endophyte DNA template (FIG. 16). The standard curve is used to quantitatively determine in planta endophyte biomass of unknown samples (FIG. 17).

A proof-of-concept study was conducted using a subset of plants which had been previously analysed using established SSR methodology. The analysis clearly shows a correlation between the quantitative SSR allele scoring and the presence of endophyte in planta (Table 12).

TABLE 12 Association between SSR-based analysis of endophyte presence and endophyte colonisation as determined by qPCR-based analysis. Each host genotype-endophyte combination represented three independent biological replicates. An SSR-based quality score was used to assess endophyte presence, a score of 3 indicated 3 out of 3 SSR markers were efficiently amplified and of the correct size. Host plant- endophyte qPCR results combination SSR-based assay (copies/ng gDNA) 1 1 Negative 2 3 16.638 3 3 68.98 4 1 Negative/very low 5 3 24.3 6 3 1.48 7 3 14.386 8 2 0.7646

EXAMPLE 4—MOLECULAR BREEDING—E1 AS A VEHICLE FOR TRAIT DELIVERY INTO PERENNIAL RYEGRASS BY HYPER-INOCULATION

-   -   Endophyte E1 is a genetically novel, non-Neotyphodiumlolii         endophyte. E1 is representative of an as yet un-named taxon     -   This supposition is supported by mitochondrial and nuclear         genome sequence analysis     -   On the basis of DNA specific content, the predicted alkaloid         profile of E1 indicates that the lolitrem B toxins deleterious         to animal health are not produced by this endophyte.     -   The E1 endophyte does not produce lolitrem B, ergovaline,         peramine, lolines or janthitrems in planta.     -   Endophyte E1 has the mating-type MAT1-1, the opposite         mating-type to that carried by all N. lolii endophytes         previously characterised     -   Endophyte E1 has a high inoculation success rate in perennial         ryegrass as compared to other endophytes     -   The identification of an endophyte of the opposite mating-type         that is highly compatible and stable in planta provides a means         for molecular breeding of endophytes for perennial ryegrass         through hyper-inoculation

Hyphal fusion between endophyte strains of the opposite mating-type provides a means for delivery of favourable traits into the host plant via hyper-inoculation. Such strains would include: 1) an endophyte strain that exhibits the favourable characteristics of high inoculation frequency and high compatibility with a wide range of elite perennial ryegrass host germplasm and; 2) an endophyte that exhibits a low inoculation frequency and low compatibility, but has a highly favourable alkaloid toxin profile.

The E1 endophyte strain is genetically novel and is compatible with a wide range of elite germplasm as it can be inoculated with a high degree of success. E1 also is of the opposite mating-type to all of the previously characterised perennial ryegrass endophytes. Molecular breeding may therefore be applied by combining the highly compatible E1 endophyte traits with the favourable toxin profile traits of endophytes such as NEA12.

The process of molecular breeding through vegetative (hyphal) fusion may occur in planta by co-inoculation of two endophyte into the same plant. However, molecular breeding may be more efficiently achieved through vegetative fusion in in vitro culture of endophytes of the opposite mating-type, followed by hyper-inoculation of the resultant endophyte.

The following experimental design is applied for molecular breeding of fungal endophytes

1. Determine vegetative compatibility of known endophytes using established co-culturing methodologies. 2. Generation of auxotrophic mutants (e.g. by gene silencing techniques such as RNAi) for two strains of endophyte, such as E1 and NEA12, exhibiting opposite mating-types. 3. Development of vegetative (hyphal) fusion protocol using a combination of cell well degrading enzymes and PEG-4000. 4. Screen for regenerated endophytes based on survival (indicating complementarity of auxotrophic mutations). 5. Genetic screen using SSR and/or mating-type markers to confirm presence of the hybrid genome in a single nuclear compartment. 6. Inoculation and compatibility/stability assessment of endophytes using established methodologies. 7. Phenotypic assessment of endophyte-host associations using established methodologies.

EXAMPLE 5—GENERATION OF ARTIFICIAL POLYPLOIDS OF FUNGAL ENDOPHYTES

Colchicine has been widely used for induction of polyploidy in plant species such as perennial ryegrass, as compared to the application to fungi, which has been limited to a few species.

The mitotic spindle inhibitor colchicine is capable of inducing autopolyploidisation, and may be applicable to the production of artificial polyploid endophytes.

Artificial polyploids were generated by colchicine induced chromosome doubling of the endophyte strains ST and NEA12.

NEA12, a janthitrem only producing endophyte, with superior bioprotective properties forms stable associations with a limited range of perennial ryegrass hosts. An artificial polyploid of NEA12 that is non-toxic to mammals, with enhanced bioprotective properties, that is broadly compatible and highly stable is highly desirable to industry.

Generation of Artificial Polyploids

Experiments were conducted to determine the range of colchicine concentrations in which the mycelia of the fungal endophyte N. lolii (strain ST) would grow successfully. Mycelia were grown in colchicine concentrations ranging from 0% to 1% for 21 days and monitored for growth (FIG. 15). At greater than or equal to 0.2% colchicine mycelium growth halted whereas at 0.1% or less colchicine mycelium growth was prolific.

Artificial polyploids were generated for endophyte strains ST and NEA12. Endophyte strains ST and NEA12 (n) were grown in 0, 0.1 and 0.2% colchicine and potato dextrose broth for 21 days followed by a 7-10 day recovery period in potato dextrose broth only. Protoplasts were generated from all colchicine concentrations and single colonies isolated (FIG. 16).

N. coenophialum strain 13E9301 and LpTG-2 strain NEA11 which are natural heteroploids (3n and 2×n fused respectively) have been utilised as control material for assessment of ploidy changes using flow cytometry. An optimised protocol was established allowing analysis of fungal protoplasts via flow cytometry. A number of colonies have been identified with changes in nuclear DNA content relative to the control samples (FIGS. 20 and 21).

TABLE 13 Summary of individual endophyte colonies, ST and NEA12, treated with colchicine and subjected to flow cytometry analysis. Colchicine Number of Number colonies Endophyte treatment (%) colonies analysed N. lolii ST 0.2 12 12 N. lolii NEA12 0.1 60 2 N. lolii NEA12 0.2 60 18

EXAMPLE 6—GENERATION OF NOVEL ENDOPHYTE VARIATION USING IONISING RADIATION Summary

-   -   Lolitrem B is the major alkaloid leading to ryegrass staggers in         grazing animals.     -   A method has been developed to eliminate the production of the         detrimental alkaloid lolitrem B, using X-ray mutagenesis induced         deletion of genes in the lolitrem B biosynthetic gene cluster,         in the ST endophyte.     -   Such an endophyte would be advantageous over existing commercial         endophytes, as ST is highly stable and broadly compatible.

Introduction

Ionising radiation is capable of introducing a broad range of mutagenic lesions and has been found to be very effective in many species. Published methods are available to readily detect deletion mutants in targeted plant genes (Li et al, 2002). Experiments have been performed to determine if N. lolii mycelia are amenable to production of mutagenic lesions by ionising radiation, in particular deletion mutations.

Generation of Novel Endophyte Variation Using Ionising Radiation

N. lolii strain ST was grown in potato dextrose broth for different periods of time ranging from 2-14 days before exposure to ionising radiation. Radiation from a caesium source was applied to the liquid cultures in doses ranging from 10-30 Gy. Following a recovery period (10-14 days) the radiation dose was repeated. Protoplasts were generated and recovery of individual colonies monitored over a 4-6 week period.

Lolitrem B is the major alkaloid leading to ryegrass staggers in grazing animals. Three genes within the lolitrem B gene cluster, which contains 10 genes all required for synthesis of lolitrem B, were targeted to identify individual N. lolii colonies with deletions (Young et al, 2005). A high throughput PCR screening method was developed to detect for the presence and absence of the three lolitrem B genes (FIG. 18).

TABLE 14 Analysis of ionising radiation experiments. Protoplast regeneration, concentration of recovered protoplasts and number of PCR analysed colonies. Endophyte Age of Dose Irradiation Protoplast Colonies PCR screened strain Culture (Gy) events regeneration Concentration plated colonies ST 2 wks  0 1 ✓  1.8 × 10⁸ pp/ml — — ST 2 wks 10 1 ✓  5.8 × 10⁵ pp/ml 700 450 ST 2 wks 15 1 ✓  7.5 × 10⁵ pp/ml 200 200 ST 2 wks 20 1 ✓  2.2 × 10⁶ pp/ml 2950  400 ST 2 wks  30* 1 — — — — ST 2 wks 30 1 ✓ 1.94 × 10⁷ pp/ml 400 350 ST 2 wks  0 2 ✓  1.1 × 10⁸ pp/ml — — ST 2 wks 10 2 ✓  2.6 × 10⁵ pp/ml 150 150 ST 2 wks 15 2 slow/reduced numbers  2.2 × 10⁷ pp/ml 200 200 ST 2 wks 20 2 ✓ 1.38 × 10⁷ pp/ml — — ST 2 wks 30/25 2 ✓ 6.38 × 10⁵ pp/ml 1000  750 ST 2 wks 30 2 ✓  1.3 × 10⁸ pp/ml 900 300 ST 4 Days  0 1 ✓  2.5 × 10⁸ pp/ml — — ST 4 Days 10 1 slow/reduced numbers 3.75 × 10⁸ pp/ml 200 200 ST 4 Days 15 1 slow/reduced numbers 1.38 × 10⁸ pp/ml 200 200 ST 4 Days 20 1 slow/reduced numbers  2.7 × 10⁵ pp/ml — — ST 4 Days 25 1 slow/reduced numbers 1.38 × 10⁵ pp/ml  50  50 ST 4 Days 30 1 slow/reduced numbers 1.38 × 10⁷ pp/ml — — Total 6950  3250  *30 Gy dose for first irradiation

EXAMPLE 7—TALL FESCUE ENDOPHYTE DISCOVERY AND CHARACTERISATION Summary Tall Fescue Endophyte Discovery

The strategies implemented for perennial ryegrass endophyte discovery were extended to the resident endophytes of tall fescue (including the FaTG-2 and FaTG-3 taxonomic groups).

A targeted collection of tall fescue germplasm was made from throughout the range of natural growth and domesticated cultivation.

A total of 568 tall fescue accessions obtained from 40 different countries were tested for endophyte incidence using endophyte-specific simple sequence repeat (SSR) genetic markers. Twelve to twenty seeds from each accession were tested for endophyte presence. Total genomic DNA was extracted from two independent seed bulks of 6-10 seeds from each accession and endophytes were detected by PCR amplification with six endophyte-specific SSR markers.

Endophyte was detected in 40% (228/568) of the tall fescue accessions tested. Furthermore, accessions from 23 out of the 40 countries screened were endophyte positive (FIG. 19) showing the highest incidence in Morocco and Pyrenees, where the majority of accessions tested (80%-100%) were endophyte positive. Accessions originating from Italy, Spain, and United States exhibited a higher endophyte incidence among the tall fescue accessions tested.

A subset of selected endophyte positive samples, were selected for further analysis using 32 endophyte-specific SSR markers. The selected genotypes represent a broad range of known geographical origins, hence representing an effective survey of tall fescue endophyte genotypic variation. A set of 52 reference isolates representing several endophyte species, including the resident endophyte of tall fescue and meadow fescue were also included to the diversity analysis.

The UPGMA phenogram, constructed using average taxonomic distance based on SSR polymorphism across 203 endophyte positive accessions, represented six different known taxa, and two out-grouped clusters (FIG. 20). The phenogram was supported by Mantel test statistics showing a high correlation coefficient (r=0.95) which indicated a high goodness-of-fit for the data. Endophytes representing six different taxa were detected in the 203 accessions (FIG. 20). The majority of endophytes (60%; 122/203) appeared to belong to the taxon Neotyphodium coenophialum, clustering in the phenogram with N. coenophialum isolates from the reference endophyte collection (FIG. 20). This species occurred in 72% (122/170) of tall fescue collection accessions.

As defined by the N. coenophialum reference isolates, the N. coenophialum cluster comprised five main sub-clusters, of which the fifth sub-cluster is rather out grouped from the other four (FIG. 20).

The genetic variation observed within N. coenophialum was high when comparing it with other taxonomic groups. In the phenogram N. coenophialum strains clustered for the most part according to their geographical origin (FIG. 20). The first sub-cluster of N. coenophialum comprised mainly tall fescue accessions from Spain (28) and few accessions from Pyrenees (3) and France (4) (FIG. 20). Italian (7) and French (14) accessions were clustered in the second sub-cluster (FIG. 20). The third sub-cluster clearly shows the genetic similarity among accessions collected from geographic area surrounding Russian Federation [Slovenia (3), Russian Federation (6), Kazakhstan (7), Former Soviet Union (4) and China (3)] (FIG. 20). Furthermore within the third sub-cluster a set of accessions from France (11) and Pyrenees (1) have formed a separate cluster from Russian Federation and its surrounding geographic origins. The fourth sub-cluster comprises only five endophytes of which two are Moroccan accessions and two are AR endophytes (AR542 and AR584) which were initially isolated from tall fescue originated in Morocco (Latch et al, 2000). The accessions collected from Portugal (4) have formed a distinct sub-cluster which is separated from all the other four sub-clusters (FIG. 20).

FaTG-2 accessions formed a cluster close, but distinct from isolates of N. lolii (FIG. 20). There were 20 FaTG-2 endophyte genotypes tall fescue collection which clustered with the FaTG-2 reference genotype. Among them, a set of six accessions formed sub-clusters having lesser genetic similarity to the FaTG-2 reference genotype. Therefore, the endophytes of those sub-clusters were named “FaTG-2 like” endophyte genotypes.

A set of six endophyte genotypes formed a distinct cluster with putative FaTG-3 reference isolates as defined by the previously-analysed AR endophytes. Furthermore, 13 accessions primarily originating from Morocco (9/13) formed a sub-cluster with putative FaTG-3 isolates and those unidentified accessions, forming a cluster distinct to putative FaTG-3 were named “FaTG-3 like” endophytes (FIG. 20).

The identities of selected putative FaTG-2 and FaTG-3 accessions are largely consistent with geographical provenance, as these taxa are known to be characteristic of populations from southern Europe and North Africa.

Two out grouped clusters were also identified and they were named as “out-group I” and “out-group II” (FIG. 20). Accessions of Mediterranean origin primarily clustered in “out-group I”, whereas one accession from Former Soviet Union formed the second out-group. Moreover, within “out-group I” Italian accessions clearly group separately from Moroccan and Algerian accessions.

A number of candidate novel endophytes have been identified.

Metabolic Profiling of Tall Fescue-Endophyte Associations

Representative tall fescue-endophyte associations were selected for metabolic profiling analysis in order to determine the endophyte derived alkaloid profile, in particular, lolitrem B, ergot alkaloids, peramine and lolines.

Analysis of metabolite production was assessed under controlled conditions using a growth chamber. Tall fescue-endophyte associations were each replicated four times by clonal splitting and arranged in a randomised block design in the growth chamber. Plants were maintained in soil for six weeks, with trimming every two weeks to encourage growth. Following 6 weeks growth, pseudostem tissue was harvested and freeze dried prior to performing a metabolite extraction and LCMS analysis. The perennial ryegrass-N. lolii designer association Bronsyn-ST was used as a control as ST is known to produce lolitrem B, ergovaline and peramine. For each of the accessions, the presence and identity of the resident endophyte was confirmed through SSR analysis of the plant material harvested for metabolic profile analysis and endophyte negative samples were removed from further analysis.

The results of the qualitative assessment alkaloid of production for 20 novel tall fescue endophytes are summarised in Table 15. Relative quantitation data for Batch three, comprising 13 endophytes assessed in their endogenous hosts, are shown in FIG. 21 and FIG. 22. A number of novel endophytes with favourable toxin profiles (low/no ergovaline production combined with loline and peramine production) have been identified.

TABLE 15 Summary of alkaloid profiles for selected tall fescue endophytes in their endogenous host. Tall fescue accession details Batch # Tall for fescue Endophyte alkaloid Alkaloid profile Confirmed accession species profiling Lolines Peramine Ergovaline* Lolitrem B profile 1 N. coenophialum 1 & 3 + + +^(M) − Y NEA13 N. coenophialum 2 n.d + + n.d n.a 3 N. coenophialum 3 + + +^(L) − n.a 4 N. coenophialum 1 n.d + + n.d n.a 5 N. coenophialum 2 n.d + + n.d n.a 6 N. coenophialum 2 n.d − + n.d n.a 7 N. coenophialum 2 & 3 + + +^(H) − Y 8 N. coenophialum 2 n.d + + n.d n.a 9 N. coenophialum 2 n.d + + n.d n.a 10 N. coenophialum 2 n.d − + n.d n.a NEA14 N. coenophialum 1 & 3 + + +^(H) − Y 12 N. coenophialum 2 & 3 + − +^(H) − Y 13 N. coenophialum 1 & 3 + + +^(L) − Y 14 N. coenophialum 2 & 3 + + +^(L) − Y 15 N. coenophialum 1 & 3 + + +^(M) − Y 16 FaTG-2 3 + + +^(M) − n.a 17 FaTG-2 2 & 3 − + +^(M) − N 18 FaTG-3 3 + + − + n.a 19 Out group 1 2 & 3 − − +^(L) − Y 20 Out group 1 1 & 3 − − +^(L) − Y ST N. lolii 3 − + + + Y *Relative quantitation of ergovaline levels: L = Low; M = Medium; H = High.

Establishment of Meristem Cultures for a Diverse Fescue Host Panel

Tissue culture responsive genotypes from selected germplasm material have been generated (Drover, Dovey, Bariane, Barolex). Table 16 shows the host cultivars, and their tissue culture responsive genotype, selected for further study. Each of the selected genotypes has a regeneration frequency greater than 80%

TABLE 16 Establishment of meristem cultures for a diverse tall fescue host panel. TCR genotype used for Cultivar inoculation Species Characteristics Bariane BARI 27 L. arundinaceum Soft leaved, later maturing, highly palatable Dovey DOV 24 L. arundinaceum High yielding, fast establishing Quantum QUAN 17 L. arundinaceum Soft leaved with improved rust resistance Jesup JESS 01 L. arundinaceum Cool season perennial forage Bronsyn BRO 08 L. perenne Standard perennial ryegrass forage type

Tall Fescue Endophyte Isolation

Selected novel endophytes were isolated from tall fescue accessions (Table 17).

TABLE 17 Summary of endophytes isolated from tall fescue accessions Endophyte Accession Origin Taxon 1 Spain N. coenophialum NEA13 N. coenophialum 4 Pyrenees N. coenophialum 5 Pyrenees N. coenophialum 6 Catalunya (Spain) N. coenophialum 7 Corsica (France) N. coenophialum 8 Corsica (France) N. coenophialum 9 Corsica (France) N. coenophialum 10 Aragon (Spain) N. coenophialum NEA14 PaySardegna (France) N. coenophialum 12 Aragon (Spain) N. coenophialum 13 Gaurda (Portugal) N. coenophialum 14 Gaurda (Portugal) N. coenophialum 15 Aragon (Spain) N. coenophialum 17 Spain FaTG-2 18 Tunisia FaTG-3 19 Algeria outgroup1 20 Sardegna (NW Italy) outgroup1 21 Catalunya (Spain) N. coenophialum

Isogenic Inoculation of Novel Tall Fescue Endophytes

A set of ten novel tall fescue endophytes were selected for inoculation based on genetic novelty using SSR-based diversity analysis and the toxin profile based on qualitative metabolic profiling (Table 18). Included in the set was the endophyte AR542 a commercial endophyte in use globally. AR542 was discovered and isolated by AgResearch NZ and is marketed as MaxP™ and MaxQ™

TABLE 18 Endophytes selected for isogenic inoculation based on analysis of genetic diversity and metabolic profile Tall fescue accession details Tall fescue Alkaloid profile acces- Endophyte Lolitrem sion species Lolines Peramine Ergovaline B NEA13 N. coenophialum n.d + + n.d  3 N. coenophialum + + +^(L) − 22 N. coenophialum n.d n.d n.d n.d NEA14 N. coenophialum + + +^(H) − 13 N. coenophialum + + +^(L) − 15 N. coenophialum + + +^(M) − 17 FaTG-2 − + +^(M) − 19 Out group 1 − − +^(L) − 20 Out group 1 − − +^(L) − AR542* N. coenophialum n.d n.d − n.d *toxin profile from Bouton et al, 2002.

In order to accurately determine the phenotypic effects of different candidate endophytes in the absence of host-specific genetic effects, a system for isogenic inoculation was used. Novel candidate endophytes were individually inoculated into elite tall fescue germplasm as well as the perennial ryegrass host genotype Bronsyn (Bro08). Following inoculation and plantlet regeneration in culture, plants were transferred to soil for three months to allow establishment of endophyte and host-plant associations. After this period, three tillers from each plant were sampled and tested for endophyte presence using SSR-based analysis.

Of the 498 isogenic inoculations tested, 109 (21.9%) could be positively scored with a high degree of confidence. Successful inoculations are listed on Table 19.

Variation in inoculation success according to candidate endophyte identity was observed. Endophyte strain 3 (4.3%), for example, exhibited relatively lower success rates as compared to strain 20 (51.1%), or the commercial endophyte AR542 (44.4%; Table 19) and only formed stable associations with one of the five hosts (Bariane). No successful inoculations were identified for endophyte strain 15. FaTG-2 endophyte, strain 17, is a highly compatible endophyte which obtains a high rate of success of inoculation into tall fescue (Table 19) compared to other endophytes examined, and is comparable to AR542. Out-group 1 endophyte strain 20 exhibits the highest level of compatibility as measured by its ability to be inoculated.

Both tall fescue endophytes inoculated into perennial ryegrass host Bro08, strain NEA13 and strain NEA14, were taken up successfully, establishing that endophyte inoculation across a range of host species is possible.

TABLE 19 Summary statistics for isogenic inoculations of selected candidate endophytes in a targeted isogenic tall fescue and perennial ryegrass panel of 5 hosts. C. Percent of successful inoculations Endophyte strain Host plant genotype 22 3 NEA13 15 NEA14 AR542 13 17 20 19 Total BARI 24 13.0 12.5  22.2 0.0  0.0 42.3 16.7 56.5 54.5  8.3 24.3 BRO 08 TBD TBD 18.2 TBD 11.8 TBD TBD TBD TBD TBD 14.3 DOV 24 30.0 0.0 TBD TBD TBD TBD TBD TBD TBD TBD 12.5 JESS 01 30.4 0.0 17.9 0.0 35.0 47.4 20.0 10.0 41.7 20.0 22.2 QUAN 17 37.5 0.0 10.0 0.0 TBD TBD TBD TBD TBD TBD 17.5 Total 25.0 4.3 17.9 0.0 13.4 44.4 18.2 41.5 51.1 13.6 21.9 Species N. coenophialum FaTG-2 Outgroup 1 TBD Be Determined

EXAMPLE 8—ANTIFUNGAL ACTIVITY OF NEOTYPHODIUM/EPICHLOË ENDOPHYTES Introduction

Neotyphodium endophytes at present are largely unexplored in terms of their production of novel antimicrobials.

While some Epichloë/Neotyphodium endophytes have been shown to inhibit the growth of plant-pathogenic fungi in vitro, the inhibitory substances produced have not been identified.

Endophytes with anti-fungal properties may benefit host plants by preventing pathogenic organisms from colonising them and causing disease. This is of particular interest to the turf grass industry.

A Bioassay to Assess Antifungal Activity of Neotyphodium Endophytes

To determine if endophytes of the species Neotyphodium produce anti-fungal substances in vitro representative species/strains from Neotyphodium were tested for the presence of anti-fungal activity against eight species of fungal plant pathogens.

Three types of inhibition reactions were observed. In the first reaction, pathogenic fungal growth was unaffected. In the second, growth of the pathogenic fungi was initially unaffected, but growth ceased when the colony margin approached a “critical” distance from the central endophyte colony. In the third stronger reaction type, the overall growth of the colony of the pathogenic fungi was reduced. Examples of inhibition reactions are shown in FIG. 23.

Variation was observed within and between endophyte taxa. Non-N. lolii strain NEA12 exhibits the strongest and most broad spectrum antifungal activity. Variation was also observed among genetically distinct strains of N. lolii. Within N. lolii, strains with strongest to weakest effects were ST>AR1>NEA3>NEA10. ST exhibited the broadest spectrum of antifungal activity, inhibiting the growth of 7/8 fungi strains tested. The bioassay results showed that endophytes in vitro exhibit variation in anti-fungal activity that does not correlate with known toxin production (specifically, lolitrem B, ergovaline and peramine). For example NEA12 does not produce lolitrem B, ergovaline and peramine and has strong antifungal activity and ST does produce lolitrem B, ergovaline and peramine and also has strong antifungal activity.

TABLE 20 Antifungal activity exhibited by representative strains of N. lolii and related endophyte taxa. Assays were scored visually from 0-5. NT—not tested. Fungal species Endophyte Endophyte Alternaria Colletrichum Rhizoctonia Trichoderma Phoma Botrytis Bipolaris Drechslera strain species alternata graminicola cerealis harzianum sorghina cinerea portulaceae brizae AR510 FaTG-3 0 0 5 1 NT NT NT NT NEA11 LpTG-2 0 1 2 0 NT NT NT NT AR1 N. lolii 0 0 3 0 2 0 1 1 NEA10 N. lolii 0 0 0 0 0 0 1 1 NEA3 N. lolii 0 0 1 1 1 0 0 0 ST N. lolii 0 1 3 2 2 2 4 3 NEA12 Non-N. lolii 3 4 4 3 3 3 3 2 Samples are scored visually from 0-5. 0 is no antifungal activity, 1 is low antifungal activity, 5 is strong antifungal activity. NT—not tested

Mass Spectrometry for Identification of Antifungal Metabolites

Mass spectrometry was used to determine the relationship between antifungal activity and metabolite expression.

Endophyte strains representing the full spectrum of antifungal activity were selected for analysis in order to identify those alkaloids that may be associated with antifungal activity (FIG. 24).

Endophyte strains were grown both in the presence and absence of the pathogenic fungi Rhizoctonia cerealis (FIG. 25). Freeze dried endophyte mycelia was then extracted for metabolic profiling analysis.

Following extraction, a validation assay was done to ensure that the alkaloids associated with antifungal activity had been appropriately extracted (FIG. 26). The antifungal activity of the extract used for LCMS analysis was confirmed. The expression of antifungal alkaloids is constitutive as extracts taken from endophyte in the absence of Rhizoctonia cerealis also exhibit antifungal activity (FIG. 26).

EXAMPLE 9—METABOLIC PROFILING Summary

Perennial ryegrass cultivars inoculated with the NEA12 endophyte were analysed using LCMS. The toxins peramine, ergovaline and lolitrem B were not detected in the extract. The AR37 metabolite 11,12-epoxy janthitrem G was detected and its structure assigned based on retention time and MS analysis of an extract of the AR37 inoculated perennial ryegrass.

Metabolic Profiling of Endophyte NEA12 in Perennial Ryegrass.

Perennial ryegrass cultivars inoculated with different endophytes were analysed for peramine (1), ergovaline (2), lolitrem B (3) and the AR37 isolated metabolites janthitrem l (4) (11,12-epoxy janthitrem G (janthitrem G (5)) by LCMS. Janthitrem G is an isomer of the previously described janthitrem F (6) and its structure was determined by NMR in the original patent describing AR37 (Latch et al, 2000; structures shown in FIG. 27).

Standards were analysed to provide reference for the perennial ryegrass analyses. The lolitrem B standard had deteriorated significantly but a peak matching the expected m/z and approximate retention time could be found (FIG. 28).

Data for AR37 inoculated endophyte and NEA12-inoculated ryegrass gave comparable results. Neither contained detectable levels of peramine, ergovaline or lolitrem B. Both contained 11,12-epoxy-janthitrem G (4) (FIG. 29). MSMS analysis of the ion m/z 646 (4) is shown in FIG. 30. The data is a good match for that described in the original patent application.

Analysis of NEA12 was carried out in a number of perennial ryegrass cultivars. It was present to a greater or lesser extent in the majority of those examined (Table 21). No attempt was made to quantitate the amount found. A standard toxic (ST) endophyte was analysed in the same perennial ryegrass cultivars. The ST endophyte produced peramine and ergovaline but not janthitrems (Table 21). The toxin profiles for ST and NEA12 are shown in FIG. 31.

TABLE 21 Analysis of endophytes in different perennial ryegrass cultivars. Perennial ryegrass cultivar/inoculation Endophyte event alkaloids detected NEA12 IMP04 20 janthitrem NEA12 TOL03 18 janthitrem NEA12 TOL03 16 janthitrem ST TOL03 01 peramine, ergovaline, lolitrem B ST TOL03 12 peramine, ergovaline, lolitrem B ST IMP04 44 peramine, ergovaline, lolitrem B ST IMP04 04 peramine, ergovaline, lolitrem B ST BRO08 02 peramine, ergovaline, lolitrem B ST BRO08 01 peramine, ergovaline, lolitrem B

The NEA12 endophyte appears to have the same alkaloid profile as AR37 and is distinctly different from the ST endophyte.

EXAMPLE 10—TALL FESCUE ENDOPHYTE DISCOVERY

The objectives of this work on discovery and characterization of endophytes in tall fescue (Lolium arundinaceum) were:

1. Identification and characterisation of novel tall fescue endophytes for evaluation in germplasm. 2. Development and evaluation of optimised associations between novel endophytes and elite germplasm.

The endophyte discovery was based on screening 568 accessions to identify endophyte positive plants followed by genotyping 210 endophytes to identify novel endophytes in tall fescue.

The characterisation in planta of novel endophytes from tall fescue was based on the following steps:

-   -   Meristem cultures for tall fescue cultivars were established for         isogenic host panel     -   Endogenous metabolic profiles were determined for 48 samples     -   Isolation of 38 endophytes was undertaken     -   Inoculation of 15-20 endophytes into isogenic host panel was         undertaken     -   Isogenic host-endophyte associations were characterised         Genotypic Analysis of Endophyte Content in Accessions from a         Targeted Fescue Germplasm Collection

Initially, 472 accessions from 30 countries were tested for endophyte incidence; with 2 replicates of 6-10 seeds in each bulk per accession used in the analysis and endophyte incidence assessed with 6 SSRs.

New accessions were included in the analysis from the under-represented geographic origins; with a total of 568 accessions from 40 countries tested for endophyte incidence.

TABLE 22 Genotypic analysis of endophyte content in accessions from a targeted fescue germplasm collection Number of Percentage positive geographic origins accessions FEtc GRIN FEtc GRIN collection collection collection collection Incidence 7 23 96% 30% assessment 01 Incidence — 10 — 45% assessment 02

Genotypic analysis of endophyte content in accessions from a targeted fescue germplasm collection is shown in Table 22. 233 endophyte positive accessions (41%) were detected. The geographical origins are represented in the endophyte incidence assessment.

A genetic diversity analysis of tall fescue endophytes is shown in FIG. 33. A selected set of 210 accessions were used to assess genetic diversity of tall fescue endophytes. Genetic diversity was assessed with 38 SSR markers. Six different taxa were detected. The majority were N. coenophialum. Twenty were FaTG-2. Six were putative FaTG-3. Thirteen were FaTG-3 like.

Diversity of host and endophyte is shown in FIG. 34.

Selection of fescue-endophyte combinations for metabolic profiling, endophyte isolation and isogenic inoculation is shown in FIG. 35. 52 accessions were initially selected for metabolic profiling and endophyte isolation. Endophyte presence was consistently detected in 25 accessions (red). An additional 48 accessions from under-represented clusters were established in the glasshouse and screened for endophyte presence. 20 accessions were endophyte positive (blue) and were selected for further analysis.

Selection of fescue-endophyte combinations for metabolic profiling, endophyte isolation and isogenic inoculation is shown in FIG. 36. Initial selections are shown in red. Additional selections are shown in blue.

The desired toxin profile of tall fescue endophytes is shown in FIG. 37.

EXAMPLE 11—METABOLIC PROFILING

The experimental design used for semi-quantitative metabolic profile analysis of tall fescue-endophyte associations for the detection of alkaloid production in the endogenous host background is described below.

A metabolic profile analysis for detection of ergovaline and peramine is shown in FIG. 38.

Endophytes selected for semi-quantitative analysis of metabolites are shown in FIG. 39.

Metabolic Profile Analysis for the Detection of Alkaloid Production of Different Fescue Endophytes

A metabolic analysis of tall fescue-endophyte associations for the detection of alkaloid production including loline, loline formate, peramine, ergovaline and lolitrem B in the endogenous host background is shown in FIG. 40. The alkaloid profile (i.e. lolines, peramine, ergovaline and lolitrem B) of tall fescue-endophyte associations in the endogenous host background for a range of endophyte strains belonging to different endophyte species is shown in Table 23.

TABLE 23 Alkaloid profile (i.e. lolines, peramine, ergovaline and lolitrem B) of tall fescue-endophyte associations in the endogenous host background for a range of endophyte strains belonging to different endophyte species (*Published data; nd = not determined). Tall fescue accession details Tall fescue Endophyte Endophyte Alkaloid profile accession strain species Lolines Peramine Ergovaline* Lolitrem B BE9301 E34 N. coenophialum + + +^(L) − 8PC NEA13 N. coenophialum n.d + + n.d FEtc7-180 NEA14 N. coenophialum + + +^(H) − FEtc7-58 NEA15 N. coenophialum + + +^(M) − FEtc7-342 NEA16 N. coenophialum + + − − FEtc7-343 NEA20 N. coenophialum + + − − 234746 NEA22 N. coenophialum + + +^(M) − FEtc6-83 NEA24 N. coenophialum + + +^(H) − FEtc7-289 NEA25 N. coenophialum + − +^(H) − FEtc6-68 NEA26 N. coenophialum + + + − FEtc6-85 NEA27 N. coenophialum n.d + + n.d FEtc6-87 NEA28 N. coenophialum n.d + + n.d FEtc7-127 NEA29 N. coenophialum + + + − FEtc6-128 NEA30 N. coenophialum + + + − FEtc6-129 NEA31 N. coenophialum + + + − 287819 NEA17 FaTG-2 − + +^(M) − 231557 NEA21 FaTG-2 + + − − 269850 NEA23 FaTG-3 + + − − 231553 NEA19 Out group 1 − − − − FEtc6-75 NEA18 Out group 1 − − − − ST ST N. lolii − + + + AR542* AR542 N. coenophialum + + − − KY31* KY31 N. coenophialum + + + − E77* E77 N. coenophialum + + + −

Further metabolic analysis of the fescue endophytes is shown in FIG. 41.

EXAMPLE 12—SEMI-QUANTITATIVE ANALYSIS OF METABOLIC PROFILE UNDER TEMPERATURE/WATER STRESS

In addition to the metabolic analysis of tall fescue-endophyte associations grown under standard conditions, for the detection of alkaloid production conferred by the endopohytes in the endogenous host background (FIGS. 38-41), a semi-quantitative analysis of metabolic profiles of tall fescue-endophyte associations grown under high temperature and water stress conditions was undertaken. Corresponding tall fescue-endophyte associations were grown under 16 h Light and 30° C.; 18 h Dark and 20° C., and then sampled for alkaloid profile analysis as described below:

-   -   Harvest (control)→freeze dry→50 mg pseudostem material→80%         methanol extraction→LCMS analysis     -   Recovery and water stress     -   Second harvest (stress)→freeze dry→SSR confirm all of the plant         material again.

This was performed in a controlled (growth chamber) environment simulating summer conditions, with light watering as required. Nine copies per accession were planted in general potting mix. A Randomized Complete Block with subsampling was used.

FIG. 42 shows a semi-quantitative analysis of metabolic profile of tall fescue-endophyte associations grown under high temperature and water stress conditions.

EXAMPLE 13—IN PLANTA ISOGENIC INOCULATION IN TALL FESCUE WITH NOVEL ENDOPHYTES Summary

A total of 36 fescue endophytes have been isolated from a range of fescue accessions from different geographic origin as described in Table 24, and found to belong to different taxa as follows: 19 of them being N. coenophialum; 5 of them being FaTG-2; 3 of them being Outgroup; 3 of them being FaTG-3; 3 of them being FaTG-3 like; and 3 of them being N. uncinatum

TABLE 24 Isolation of fungal endophyte cultures from endophyte-containing fescue accessions Establishment of Meristem Cultures for Diverse Host Panel for In Planta Inoculation of Fescue Endophytes Fescue Endophyte Accession Strain Origin Cluster Taxon 1 8PC 8PC C01.1 N. coenophialum 2 BE9301 E34 C01.1 N. coenophialum 3 E77 E77 C01.2 N. coenophialum 4 FEtc6-62 Catalunya (Spain) 4 C01.2 N. coenophialum 5 FEtc6-68 NEA26 Catalunya (Spain) 14 C01.2 N. coenophialum 6 FEtc7-127 NEA29 Aragon (Spain)14 C01.2 N. coenophialum 7 FEtc7-289 NEA25 Aragon (Spain)14 C01.2 N. coenophialum 8 FEtc7-58 NEA15 Aragon (Spain) 1 C01.2 N. coenophialum 9 234746 NEA22 Spain C01.2 N. coenophialum 10 632582 Italy C02.1 N. coenophialum 11 Kentucky 31 KY31 C02.1 N. coenophialum 12 FEtc6-128 NEA30 Pyrenees13 C02.2 N. coenophialum 13 FEtc6-129 NEA31 Pyrenees17 C02.2 N. coenophialum 14 FEtc7-180 NEA14 PaySardegna (Basque (Fran

C02.2 N. coenophialum 15 440364 Kazakhstan C03 N. coenophialum 16 619005 China C03 N. coenophialum 17 FEtc6-83 NEA24 Corsica (France)7 C04 N. coenophialum 18 FEtc6-85 NEA27 Corsica (France) 15 C04 N. coenophialum 19 FEtc6-87 NEA28 Corsica (France) 17 C04 N. coenophialum 20 AR542 AR542 Morocco C05 N. coenophialum 21 FEtc7-342 NEA16 Gaurda (Portugal) C06 N. coenophialum 22 FEtc7-343 NEA20 Gaurda (Portugal) C06 N. coenophialum 23 231557 NEA21 Morocco C09 FaTG-2 24 287819 NEA17 Spain C09 FaTG-2 25 598834 Morocco C09 FaTG-2 26 231559 Morocco C09 FaTG-2 27 598852 Morocco C09 FaTG-2 28 598934 Italy C10 Outgroup 29 231553 NEA19 Algeria C10 Outgroup 30 FEtc6-75 NEA18 Sardegna (NW Italy) 5 C10 Outgroup 31 269850 NEA23 Tunisia C12 FaTG-3 32 610918 Tunisia C12 FaTG-3 33 610919 Tunisia C12 FaTG-3 34 598829 Morocco C13 FaTG-3 like 35 598863 Morocco C13 FaTG-3 like 36 598870 Morocco C13 FaTG-3 like 37 M311046 Russion Federation C14 N. uncinatum 38 M595026 United Kingdom C14 N. uncinatum 39 M611046 Russion Federation C14 N. uncinatum

indicates data missing or illegible when filed

Table 25 shows selected tall fescue and perennial ryegrass cultivars used to identify representative plant genotypes included in the diverse host panel for in planta inoculation of fescue endophytes. All the selected plant genotypes have a high regeneration frequency of >80%.

TABLE 25 Selected tall fescue and perennial ryegrass cultivars used to identify representative plant genotypes included in the diverse host panel for in planta inoculation of fescue endophytes Genotype Cultivar code Species Characteristics Bariane BARI 27 L. arundinaceum Soft leaved, later maturing, highly palatable Dovey DOV 24 L. arundinaceum High yielding, fast establishing Quantum QUAN 17 L. arundinaceum Soft leaved with improved rust resistance Jesup JES 01 L. arundinaceum Cool season perennial forage Bronsyn BRO 08 L. perenne Standard perennial ryegrass forage type

Isolated fungal endophytes from endophyte-containing fescue accessions selected for in planta isogenic inoculation into the diverse host panel are shown in FIG. 43. FIG. 44 shows SSR-based genotyping of isolated endophyte cultures prior to in planta isogenic inoculation to confirm their identity.

Results from the SSR genotyping indicating the allele number and sizes for different SSR markers for the different fescue endophyte strains are shown in Table 26.

TABLE 26 Presence of alleles in endophyte strains Endophyte Tall Fescue NCESTA1DH04 (FAM) NLESTA1TA10 (FAM) NCESTA1HA02 (HEX) NCESTA1CC10 (HEX) Strain ID Accession ID Allele 1 Allele 2 Allele 3 Allele 1 Allele 2 Allele 3 Allele 1 Allele 2 Allele 3 Allele 1 Allele 2 Allele 3 AR542 — 212 218 227 165 175 322 327 330 198 201 211 E34 BE_9301 212 218 224 165 175 322 329 330 198 201 211 E77 — 212 218 224 165 175 308 322 330 197 201 211 NEA13 8PC 212 218 224 165 175 322 330 197 200 210 NEA14 FEtc7-180 215 218 229 165 175 322 329 330 198 201 NEA15 FEtc7-58 212 218 224 165 175 322 329 330 197 201 211 NEA16 FEtc7-342 215 227 165 175 309 322 330 198 201 211 NEA17 287819 215 221 227 171 175 322 201 203 NEA18 FEtc6-75 218 227 171 175 304 322 201 NEA19 231553 221 227 171 175 304 325 201

Results from the in planta isogenic inoculation into the diverse host panel of selected isolated fungal endophytes from endophyte-containing fescue accessions are shown in Table 27. Data on number of inoculations tested, number of successful inoculations and % of successful inoculations are provided in Table 6 to illustrate the inoculation ability of tall fescue endophytes in tall fescue and perennial ryegrass hosts.

TABLE 27 Inoculation Ability of Tall Fescue Endophytes in Tall Fescue and Perennial Ryegrass Hosts E77 E34 NEA13 NEA15 NEA14 AR542 NEA16 NEA17 NEA18 NEA19 E77 BE9301 8PC Fetc7-58 FEtc7-180 AR542 FEtc7-342 287819 FEtc6-75 231553 Total A. Number of inoculations tested BARI 27 23 25 30 34 38 38 24 32 40 27 311 BRO 08 39 31 24 27 35 36 30 33 48 22 325 DOV 24 10 14 NI NI NI 17 8 18 14 16 97 JESS 01 23 23 39 27 20 36 33 17 28 14 260 QUAN 17 8 31 20 15 17 21 18 16 15 8 169 Total 103 124 113 103 110 148 113 116 145 87 1162 B. Number of successful inoculations BARI 27 3 3 4 0 1 11 3 17 18 2 62 BRO 08 0 0 2 0 2 0 0 4 2 5 15 DOV 24 3 0 NI NI NI 1 0 1 4 0 9 JESS 01 7 0 5 0 7 10 3 2 1 2 37 QUAN 17 3 0 1 0 0 0 0 6 5 3 18 Total 16 3 12 0 10 22 6 30 30 12 141 C. Percent of successful inoculations BARI 27 13.0 12.0 13.3 0.0 2.6 28.9 12.5 53.1 45.0 7.4 18.8 BRO 08 0.0 0.0 8.3 0.0 5.7 0.0 0.0 12.1 4.2 22.7 5.3 DOV 24 30.0 0.0 NI NI NI 5.9 0.0 5.6 28.6 0.0 10.0 JESS 01 30.4 0.0 12.8 0.0 35.0 27.8 9.1 11.8 3.6 14.3 14.5 QUAN 17 37.5 0.0 5.0 0.0 0.0 0.0 0.0 37.5 33.3 37.5 15.1 Total 22.2 2.4 9.9 0.0 10.8 12.5 4.3 24.0 22.9 16.4 12.7 Cluster 1 1 1 1 2 3 3 7 8 8 Species N. coenophialum FaTG-2 Outgroup 1 NI Not inoculated

EXAMPLE 14—ENDOPHYTE VEGETATIVE STABILITY IN TALL FESCUE AND PERENNIAL RYEGRASS HOST GENOTYPES

Following in planta isogenic inoculation with a range of selected isolated endophytes from fescue accessions, the endophyte vegetative stability of these endophytes in the different tall fescue and perennial host genotypes (i.e. BRO 08, BARI 27, DOV 24) was assessed, showing that:

-   -   Several tall fescue endophytes (e.g. NEA17, NEA18, NEA19) were         stable in perennial ryegrass (BRO08).     -   BAR127 formed stable associations with all endophytes except for         NEA15.     -   NEA15 failed to form stable associations with any of host         genotypes tested.     -   DOV24 formed few stable associations.

The stability of these associations of novel tall fescue endophytes inoculated in different tall fescue and perennial ryegrass genotypes from the diverse host panel was assessed 12 months post-inoculation. Corresponding results are shown in Table 28.

TABLE 28 Stability of associations of novel tall fescue endophytes (e.g. NEA13, NEA14, NEA15, NEA16, NEA17, etc.) inoculated in different tall fescue and perennial ryegrass genotypes (BARI 27, BRO 08, DOV 24, JESS 01 and QUAN 17) from the diverse host panel assessed 12 months post-inoculation. NA—not applicable, NI—not inoculated, number of stable association/number of associations NEA15 NEA14 NEA16 NEA18 Plant E77 E34 NEA13 Fetc7- FEtc7- AR542 Fetc7- NEA17 FEtc6- NEA19 Genotype E77 BE9301 8PC 58 180 AR542 342 287819 75 231553 BARI 27 1/2 2/2 1/4 NA 1/1 7/7 1/1 1/2 8/10 1/1 BRO 08 NA NA 0/1 NA 0/2 NA NA 5/5 2/2 3/5 DOV 24 1/2 NA NI NI NI 0/1 NA 2/2 2/4 NA JESS 01 5/5 NA 4/6 NA 5/6 5/10 2/3 0/1 0/1 3/3 QUAN 17 2/3 NA 0/1 NA NA NA NA 3/6 3/5 1/2

FIG. 45 shows stability at 12 months post inoculation of selected endophytes in tall fescue and perennial ryegrass host genotypes from the diverse host panel.

The range of novel fescue endophytes selected for in planta isogenic inoculation is shown in FIG. 46.

Table 29 shows additional novel tall fescue endophytes (e.g. NEA20, NEA21, NEA22, etc.) selected for in planta isogenic inoculations in tall fescue genotypes (i.e. BARI 27, JESS 01 and QUAN 17) from the diverse host panel, based on the following selection criteria:

-   -   1. Produce little or no ergovaline     -   2. Produce no lolitrem B     -   3. Produce lolines and/or peramine

TABLE 29 Additional novel tall fescue endophytes (e.g. NEA20, NEA21, NEA22, etc.) selected for in planta isogenic inoculations in tall fescue genotypes (i.e. BARI 27, JESS 01 and QUAN 17) from the diverse host panel. Nco = N. coenophialum; ? = alkaloid profile not tested; TBI = To Be Inoculated. NEA20 NEA21 NEA22 NEA23 NEA24 NEA27 NEA30 FEtc7- FEtc6- FEtc6- FEtc6- 343 231557 234746 269850 83 85 128 Nco FaTG-3 Nco FaTG-3 Nco Nco Nco Lol/—/P/— Lol/—/P/— Lol/E/P/— Lol/—/P/— Lol/E/P/— ?/E/P/? ?/E/P/? BARI 28 30 30 TBI 30 25 30 27 JESS 23 20 20 TBI 20 20 30 01 QUAN 30 30 40 TBI 30 35 25 17

EXAMPLE 15—METABOLIC PROFILING OF ENDOPHYTE-TALL FESCUE ASSOCIATIONS ESTABLISHED FOLLOWING IN PLANTA ISOGENIC INOCULATIONS OF NOVEL TALL FESCUE ENDOPHYTES IN TALL FESCUE GENOTYPES FROM THE DIVERSE HOST PANEL

Metabolic profiling of endophyte-tall fescue associations established following in planta isogenic inoculations of novel tall fescue endophytes in tall fescue genotypes from the diverse host panel is shown in FIGS. 47, 49 and 50. These figures:

-   -   Compare semi-quantitative alkaloid profiles of selected         endophytes across different isogenic hosts     -   Compare semi-quantitative alkaloid profiles for diverse         endophytes in an isogenic host     -   Compare semi-quantitative alkaloid profiles of tall fescue and         perennial ryegrass endophytes in the perennial ryegrass genotype         Bro08

FIG. 48 shows the presence of peramine and ergovaline in endophyte-tall fescue associations established following in planta isogenic inoculations of novel tall fescue endophytes in tall fescue genotypes from the diverse host panel.

Table 30 shows metabolic profiling of endophyte-tall fescue associations established following in planta isogenic inoculations of novel tall fescue endophytes in tall fescue genotypes from the diverse host panel. Confirmed endophyte positive (E+) plants were split to 5 replicates and regularly trimmed to promote tillering. Four months later E+ plants were re-potted in 12 replicates. One month later E+ plants were re-potted if less than 9 positive copies were available at the time. Endophyte status was tested using SSR markers after each re-potting.

TABLE 30 Endophyte-tall fescue associations established following in planta isogenic inoculations of novel tall fescue endophytes in tall fescue genotypes from the diverse host panel used for metabolic profiling. Endophyte genotype NEA19 NEA17 E34 Host genotypes 231553 287819 8PC AR542 BE9301 Bariane (Bari27) 2/5 2/5 3/3 11/11 3/3 10/11 5/5 10/10 1/4 8/12 Dovey (DOV 24) NA 2/5 8/8 NA NA NA Jessup (Jess01) 2/4 4/8 NA 3/3 12/12 4/4 12/12 NA Quantum (Quan17) 2/5 8/7 4/5 12/12 NA NA Bronsyn (Bro08) 9/9 10/11 5/5 11/12 1/9 0/8 NA Endophyte genotype NEA18 NEA14 NEA16 NEA15 Host genotypes E77 FEtc6-75 Fetc7-180 Fetc7-342 Fetc7-58 Bariane (Bari27) NA 9/14 5/5 12/12 3/4 5/12 1/4 1/6 16/25 Dovey (DOV 24) 3/5 6/12 3/5  3/12 NA NA NA Jessup (Jess01) 2/3 8/11 NA 2/4 7/19 2/3 12/12 NA Quantum 4/5 12/12  2/4  5/12 NA NA NA (Quan17) Bronsyn (Bro08) NA 3/4 7/7 0/5 NA NA

A range of endophyte-tall fescue associations established following in planta isogenic inoculations of novel tall fescue endophytes in tall fescue genotypes from the diverse host panel were selected for metabolic profiling (Table 30). In total, 29 isogenic host-endophyte associations were subject to LCMS analysis, following the experimental design described below:

Experimental Design

-   -   Trim and re-pot plants     -   16 h Light, 30° C.; 18 h Dark, 20° C.     -   Harvest (control)→freeze dry→50 mg pseudostem material→80%         methanol extraction→LCMS analysis     -   Recovery and water stress     -   Second harvest (stressed)→freeze dry→50 mg pseudostem         material→80% methanol extraction→LCMS analysis.

This was performed in a controlled (growth chamber) environment simulating summer conditions, with light watering as required. Nine copies per accession were planted in general potting mix. A Randomized Complete Block with subsampling was used.

EXAMPLE 16—BIO-PROTECTIVE PROPERTIES OF FESCUE ENDOPHYTES

Three fungal pathogens (i.e. Colletrotrichum graminicola, Drechslera brizae and Rhizoctonia cerealis)—causing a range of fungal diseases and infecting a range of different plant hosts—were included in antifungal bioassays used to analyse the potential anti-fungal activities of isolated fescue endophytes. FIG. 51 shows results from anti-fungal bioassays of isolated fescue endophytes. Results of anti-fungal bioassays are also shown in Table 31. A range of endophytes were found to have high (H) and medium (M) antifungal activity (Table 31).

TABLE 31 Anti-fungal bioassays of isolated novel fescue endophytes Tall Fescue endophytes Antifungal activity against Strain ID Accession Taxon Colletotrichum graminicola Drechslera brizae Rhizoctonia cerealis 1 440364 N. coenophialum H H H 2 AR542 AR542 N. coenophialum M H H 3 E34 BE9301 N. coenophialum M M H 4 NEA13 8PC N. coenophialum M H H 5 NEA14 FEtc7-180 N. coenophialum M M H 6 NEA15 FEtc7-58 N. coenophialum M H H 7 NEA16 FEtc7-342 N. coenophialum M H H 8 NEA22 234746 N. coenophialum H M M 9 NEA27 FEtc6-85 N. coenophialum L M L 10 NEA30 FEtc6-128 N. coenophialum M H H 11 E1 Non-N. lolii L L M 12 NEA18 FEtc6-75 Outgroup 1 M H H 13 598852 FaTG-2 M H H 14 610918 FaTG-3 M H H 15 NEA21 231557 FaTG-3 M H M 16 598829 FaTG-3 like M L M Antifungal activity: Low, Medium, High

EXAMPLE 17—GENOME SURVEY SEQUENCING OF NOVEL TALL FESCUE ENDOPHYTES

A range of novel tall fescue endophtyes were subjected to genome survey sequencing (GSS).

FIG. 52 shows a strategy for GSS of selected novel fescue endophytes. The alkaloid profiles of novel fescue endophytes subjected to GSS analysis are shown in Table 32.

TABLE 32 Alkaloid profiles of sequenced endophytes. Tall fescue accession details Accession Alkaloid Endophyte No/isolated Endophyte profile in Endogenous Host strain ID species Lolines Peramine Ergovaline Lolitrem B E34 BE9301 N. coenophialum + + + − NEA13 8PC N. coenophialum ND + + ND NEA14 FEtc7-180 N. coenophialum + + + − NEA15 FEtc7-58 N. coenophialum + + + − NEA16 FEtc7-342 N. coenophialum + + − − NEA20 FEtc7-343 N. coenophialum + + − − NEA22 234746 N. coenophialum + + + − NEA24 FEtc6-83 N. coenophialum + + + − NEA17 287819 FaTG-2 − + + − NEA21 231557 FaTG-3 + + − − NEA23 269850 FaTG-3 + + − − NEA19 231553 non-Epichloe − − − − out-group NEA18 FEtc6-75 non-Epichloe − − − − out-group AR542* AR542* N. coenophialum + + − − E77* E77* N. coenophialum + + + − 598852 598852 FaTG-2 ND ND ND ND AR501* AR501* FaTG-3 + + − − 598829 598829 FaTG-3 like ND ND ND ND E81 E81 N. uncinatum ND ND ND ND 9340 9340 E. typhina ND ND ND ND 9707 9707 E. baconii ND ND ND ND + Alkaloid present, − Alkaloid absent, ND: alkaloid profile not determined *Profiles are taken from published data

FIG. 53 shows the peramine biosynthetic pathway. PerA encodes a single multifunctional enzyme that catalyses all the biosynthetic steps. GenBank accession Number: AB205145. The presence of the perA gene in non-Epichloe out-group endophytes is shown in FIG. 54.

FIG. 55 shows the ergovaline biosynthetic pathway. Genes in the eas gene cluster which are involved in ergovaline biosynthesis are shown in FIG. 56 and Table 33. The dmaW gene encodes DMAT synthase enzyme, which catalyzes the first committed step in ergovaline biosynthesis. Presence of the dmaW gene in novel fescue endophytes is shown in FIG. 57 and presence of the eas gene cluster in novel fescue endophytes is shown in FIG. 58.

TABLE 33 Genes in the eas cluster Gene Cluster Gene GenBank Accession No dmaW AY259838 eas gene cluster easA EF125025 easE EF125025 easF EF125025 easG EF125025 easH EF125025 IpsA AF368420 IpsB EF125025

FIG. 59 shows the Lolitrem B biosynthetic pathway. Genes in the gene cluster which are involved in Lolitrem B biosynthesis are shown in FIG. 60 and Table 34. Presence of gene cluster 1 (ItmG, ItmM and ItmK) in endophytes is shown in FIG. 61, presence of gene cluster 2 (ItmB, ItmQ, ItmP, ItmF and ItmC) is shown in FIG. 62 and presence of gene cluster 3 (ItmE and ItmJ) is shown in FIG. 63.

TABLE 34 Genes in the gene cluster involved in Lolitrem B biosynthesis Gene Cluster Gene GenBank Accession No gene cluster 01 ItmG AY742903 ItmM AY742903 ItmK AY742903 gene cluster 02 ItmB DQ443465 ItmQ DQ443465 ItmP DQ443465 ItmF DQ443465 ItmC DQ443465 gene cluster 03 ItmJ DQ443465 ItmE DQ443465

FIG. 64 shows the Loline biosynthetic pathway. Genes in the gene cluster which are involved in Loline biosynthesis are shown in FIG. 65 and Table 35. Presence of Loline biosynthetic gene cluster in novel fescue endophytes is shown in FIG. 66.

TABLE 35 Genes in the Loline biosynthetic gene cluster Gene Cluster Gene GenBank Accession No LOL gene cluster lolF EF012269 lolC EF012269 lolD EF012269 lolO EF012269 lolA EF012269 lolU EF012269 lolP EF012269 lolT EF012269 lolE EF012269

FIG. 67 shows an alkaloid biosynthetic gene analysis for endophyte strain NEA23. Tables 36 and 37 show alkaloid biosynthetic gene analyses for various endophyte strains. Table 36 shows results from the assessment of alkaloid biosynthetic gene presence/absence for different endophytes by mapping genome survey sequence reads corresponding to the different alkaloid biosynthetic genes/gene clusters.

Table 37 shows results from the assessment of alkaloid biosynthetic gene presence/absence for different endophytes by mapping genome survey sequence reads corresponding to the different alkaloid biosynthetic genes/gene clusters as well as corresponding alkaloid profile observed for corresponding tall fescue-endophyte associations.

Table 38 shows novel fescue endophytes (NEA16, NEA18, NEA19, NEA20, NEA21 and NEA23) with favourable toxin profiles.

TABLE 38 Novel fescue endophytes (NEA16, NEA18, NEA19, NEA20, NEA21 and NEA23) with favourable toxin profiles and antifungal activities observed in bioassays. Tall fescue Alkaloid profile accession Taxon (Lol/P/E/L) Antifungal NEA21 FaTG-3 +/+/−/− High NEA23 FaTG-3 +/+/−/− Not tested AR501* FaTG-3 +/+/−/− — NEA18 Non-Epichloë −/−/−/− High Outgroup NEA19 Non-Epichloë −/−/−/− Not tested Outgroup NEA16 N. coenophialum +/+/−/− High NEA20 N. coenophialum +/+/−/− Not tested AR542* N. coenophialum +/+/−/− — *Control commercial endophyte

A genotypic analysis of the novel fescue endophytes NEA23 and NEA21 is shown in FIG. 68.

EXAMPLE 18—OVERVIEW OF GENERATION OF NOVEL DESIGNER NEOTYPHODIUM ENDOPHYTE VARIANT STRAINS THROUGH MUTAGENESIS

The objective of this work was to create novel variants of the perennial ryegrass endophyte, Neotyphodium lolii, through induced polyploidisation and mutagenesis, with desirable properties such as enhanced bioactivities (e.g. antifungal acitivity), and/or altered plant colonization ability and stability of grass host-endophyte variant associations (e.g. altered in vitro growth), and/or altered growth performance (e.g. enhanced plant vigour, enhanced drought tolerance, enhanced water use efficiency) of corresponding grass host-endophyte variant associations. These grass host-endophyte variant associations are referred to as novel ‘designer’ grass-endophyte associations.

Experimental Strategies for the Generation and Characterisation of Novel Designer Neotyphodium Endophyte Variant Strains Through Mutagenesis

The experimental activities thus included:

1. Establishment of phenotypic screens for novel ‘designer’ grass-endophyte associations such as:

-   -   Enhanced biotic stress tolerance     -   Enhanced drought tolerance and enhanced water use efficiency     -   Enhanced plant vigour         2. Targeted generation (i.e. polyploidisation and X-ray         mutagenesis) and characterisation (i.e. antifungal bioassays, in         vitro growth rate, genome survey sequencing [GSS]) of novel         ‘designer’ endophytes         3. Breeding of ‘designer’ grass-endophyte associations     -   Delivery of ‘designer’ endophytes into grass (e.g. perennial         ryegrass) germplasm development process.

EXAMPLE 19—ESTABLISHMENT OF PHENOTYPIC SCREENS FOR NOVEL ‘DESIGNER’ GRASS-ENDOPHYTE ASSOCIATIONS

Assessment of enhanced biotic stress tolerance using NEA12 is shown in FIGS. 71 and 72. FIG. 71 shows in vitro bioassays to assess antifungal activity of Neotyphodium endophytes. FIG. 72 shows a detached leaf assay to assess resistance to crown rust (Puccinia coronata f. sp. lolii).

Assessment of enhanced drought tolerance and enhanced water use efficiency is shown in FIG. 73. This involved glasshouse and field trial screens for drought tolerance, survival and recovery, regrowth after drought, metabolic profiling and detailed phenotypic characterisation including multiple trait dissection (based on assessments and measurements associated with plant morphology, plant physiology, plant biochemistry).

EXAMPLE 20—GENERATION OF DESIGNER N. LOLII GENOTYPES BY POLYPLOIDISATION

This involved creation of novel variation in Neotyphodium endophytes without the use of transgenic technology. Colchicine has been widely and successfully used for chromosome doubling in plants, e.g. perennial ryegrass. It inhibits chromosome segregation during mitosis inducing autopolyploidisation (chromosome doubling; see FIG. 74). This enables the generation of novel endophytes through induced chromosome doubling and may be applicable to the production of artificial polyploid endophytes.

The experimental work flow for chromosome doubling is shown in FIG. 75.

Flow cytometry calibrations to assess DNA content in Neotyphodium endophytes are shown in FIG. 76. Peaks indicate relative nuclear DNA content.

Flow cytometry analysis of NEA12^(dh) strains is shown in FIG. 77 and Table 39.

1. ST endophyte strain is highly stable, broadly compatible and produces lolitrems, peramine and ergovaline. 2. NEA12 endophyte strain produces janthitrem only. 3. AR1 produces peramine only.

TABLE 39 Colchicine treated endophyte strains (ST, NEA12 and AR1 endophyte strains) subjected to colchicine treatments (at different colchicine concentrations in %) leading to the recovery of endophyte colonies (# of colonies) used for flow cytometry analysis # colonies Endophyte Colchicine treatment (%) # of colonies analysed N. lolii ST 0.2 12 12 N. lolii NEA12 0.1 60 2 N. lolii NEA12 0.2 60 18 N. lolii AR1 0.1 60 0 N. lolii AR1 0.2 60 0

EXAMPLE 21—ANALYSIS OF IN VITRO GROWTH OF NEA12^(DH) NEOTYPHODIUM VARIANT ENDOPHYTE STRAINS

Analysis of growth rate of NEA12^(dh) Neotyphodium variant endophyte strains in in vitro culture after 8 weeks is shown in FIG. 78. In an initial screen, analysis of variance identified two NEA12^(dh) Neotyphodium variant endophyte strains (NEA12^(dh17) and NEA12^(dh4)) showing significantly different in vitro growth rate to the control NEA12 endophyte:

NEA12^(dh17) grows significantly faster (p<0.01**) NEA12^(dh4) grows significantly slower (p<0.05*)

Analysis of growth rate of NEA12^(dh) Neotyphodium variant endophyte strains in in vitro culture over 5 weeks is shown in FIG. 10. In a validation screen, Student's t-tests identified two NEA12^(dh) Neotyphodium variant endophyte strains (NEA12^(dh17) and NEA12^(dh15)) showing significantly different in vitro growth rate to the control NEA12 endophyte:

NEA12^(dh17) grows significantly faster (p<0.01**) NEA12^(dh15) grows significantly slower (p<0.01**)

EXAMPLE 22—ANTIFUNGAL BIOASSAYS OF NEA12^(DH) NEOTYPHODIUM VARIANT ENDOPHYTE STRAINS

A list of fungal pathogens (causing a range of fungal diseases and infecting a range of different plant hosts) that were included in antifungal bioassays used to analyse NEA12^(dh) Neotyphodium variant endophyte strains to assess their spectrum of antifungal activities is shown in Table 40.

TABLE 40 Fungal pathogens (causing a range of fungal diseases and infecting a range of different plant hosts) included in antifungal bioassays to analyse NEA12^(dh) Neotyphodium variant endophyte strains to assess their spectrum of antifungal activities Fungus Disease Hosts Alternaria alternata leaf spot, rot, blight Numerous (dead plant materials) Bipolaris portulacae Damping-off Asteraceae (daisies), Portulacaceae (purslane) Botrytis cinerea Stem rot, mould, Many dicots, few seedling wilt monocots Colletotrichum Leaf spot, stalk rot Poaceae (especially graminicola Zea mays) Drechslera brizae Leaf blight Poaceae (Briza spp.) Phoma sorghina Spot (leaf, glume, seed), Poaceae (grasses) Root rot, Dying-off Rhizoctonia cerealis Spot (wheat) Poaceae (grasses) Yellow patch (turfgrass) Trichoderma Green mould, Many dicots, few harzianum Parasite of other fugni monocots, Fungi

Antifungal bioassays of NEA12^(dh) Neotyphodium variant endophyte strains are shown in FIGS. 80 and 81. Twenty NEA12^(dh) strains were screened for changes in antifungal activity. Four NEA12^(dh) strains (i.e. dh5, dh6, dh13 and dh14) were identified as having greater antifungal activity compared to NEA12.

EXAMPLE 23—GENOME SURVEY SEQUENCING AND SEQUENCE ANALYSIS OF NEA12^(DH) NEOTYPHODIUM VARIANT ENDOPHYTE STRAINS

NEA12^(dh) Neotyphodium variant endophyte strains with enhanced antifungal activity, showing faster in vitro growth rate and higher DNA content were subjected to genome survey sequencing (GSS). Sequence data was generated for 10 NEA12^(dh) strains and control NEA12 strain (highlighted in blue on Table 41).

Genome survey sequencing (GSS) data obtained for NEA12^(dh) Neotyphodium variant endophyte strains derived from colchicine treated NEA12 control strain (highlighted in blue on Table 41) were analysed as follows:

-   -   De-novo assembly of the GSS data from NEA12 control strain—to         act as a reference genome sequence for the analysis of the         NEA12^(dh) Neotyphodium variant endophyte strains     -   Map the GSS data sequence reads from the NEA12^(dh) Neotyphodium         variant endophyte strains to the NEA12 reference genome sequence     -   Identify potentially duplicated regions, i.e. regions with         higher than expected sequence coverage     -   Identify gene sequences that may have been duplicated

Analysis of GSS read depth of NEA12^(dh) Neotyphodium variant endophyte strains is shown in FIG. 82. Analysis of sequence contigs that appeared to have higher than expected read depth indicates that no major duplication event has occurred (excepting whole genome events). The patterns of read depth across these contigs are not identical between strains. This suggests there are differences between the NEA12^(dh) Neotyphodium variant endophyte strains and the control NEA12 strain.

Analysis of GSS sequence assemblies for the NEA12^(dh) Neotyphodium variant endophyte strains and the control NEA12 strain is shown in Table 42.

TABLE 42 Analysis of GSS sequence assemblies for the NEA12^(dh) Neotyphodium variant endophyte strains and the control NEA12 strain Strain # contigs N50 Max contig # bases NEA12 143202 28621 181461 32734984 NEA12dh5 305031 29444 191191 30994592 NEA12dh17 274394 37802 209957 30777017 NEA12dh18 282692 30717 177813 30889903

Independent de novo sequence assemblies were performed using parameters identical to those used in assembling the genome sequence for the control NEA12 endophyte strain. Differences in sequence assembly statistics may indicate genomic differences between strains. GSS data obtained for the NEA12^(dh) Neotyphodium variant endophyte strains and used in the sequence assemblies reveal fewer bases incorporated into the sequence assembly and produce more sequence contigs. Increased numbers of smaller sequence contigs may be caused by transposon movement/replication.

Analysis of sequence reads mapping to the NEA12 genome sequence assembly is shown in FIG. 83. While we do not wish to be restricted by theory, if the genomes were the same no difference in the number of sequence reads mapping to the reference genome sequence would be expected. NEA12^(dh) Neotyphodium variant endophyte strains range from 35-70% sequence reads mapping to NEA12 sequence contigs >5 kb in size. There are differences between the genome sequences of the NEA12^(dh) Neotyphodium variant endophyte strains and the control NEA12 strain.

Summary of Results on Generation and Characterisation of Novel Designer Neotyphodium Variant Endophyte Strains Through Colchicine Treatment Based Mutagenesis

Sequence read depth changes were analysed in NEA12^(dh) Neotyphodium variant endophyte strains compared with the control NEA12 strain. Whilst no large partial genome sequence duplication events were detected, the occurrence of full genome duplication events in the NEA12^(dh) Neotyphodium variant endophyte strains cannot be excluded based on the GSS sequence analysis.

De novo sequence assemblies were independently performed on GSS data obtained from the NEA12^(dh) Neotyphodium variant endophyte strains. Differences in sequence assembly statistics indicate that genomic changes were caused by the colchicine-treatment in the NEA12^(dh) Neotyphodium variant endophyte strains. The number of sequence reads from NEA12^(dh) Neotyphodium variant endophyte strains mapping to the NEA12 reference genome sequence varies between strains. All GSS data analyses performed on the NEA12^(dh) Neotyphodium variant endophyte strains indicate genomic differences.

In summary, the following novel designer endophytes were generated by colchicine treatment of NEA12 endophytes:

-   -   Four NEA12^(dh) Neotyphodium variant endophyte strains (dh5,         dh6, dh13 and dh14) with enhanced bioprotective properties (i.e.         antifungal bioactivities);     -   One NEA12^(dh) Neotyphodium variant endophyte strain (dh17) with         higher in vitro growth rate than control NEA12 strain (i.e.         potentially with enhanced stability/host colonization ability);     -   Ten NEA12^(dh) Neotyphodium variant endophyte strains (including         dh5, dh6, dh13, dh14 and dh17) and control NEA12 strain         subjected to genome survey sequencing; and     -   Five NEA12^(dh) Neotyphodium variant endophyte strains         (including dh5, dh13 and dh17) selected and subjected to         isogenic inoculation in planta.

EXAMPLE 24—IN PLANTA ISOGENIC INOCULATION IN PERENNIAL RYEGRASS WITH NEA12^(DH) NEOTYPHODIUM VARIANT ENDOPHYTE STRAINS

The following NEA12^(dh) Neotyphodium variant endophyte strains and control NEA12 strain were used for in planta isogenic inoculation in perennial ryegrass:

-   -   NEA12     -   NEA12dh5 showing higher antifungal activity than control NEA12     -   NEA12dh13 showing higher antifungal activity than control NEA12     -   NEA12dh4 showing slower in vitro growth rate than control NEA12     -   NEA12dh15 showing slower in vitro growth rate than control NEA12     -   NEA12dh17 showing faster in vitro growth rate than control NEA12

TABLE 43 Isogenic inoculation of perennial ryegrass genotypes (IMP04 and TOL03) with NEA12dh Neotyphodium variant endophyte strains. Numbers indicate number of perennial ryegrass plants of the two genotypes subjected to isogenic inoculation with the different NEA12dh Neotyphodium variant endophyte strains. NEA12 NEA12 NEA12 NEA12 NEA12 Plant Genotype dh4 dh5 dh13 dh15 dh17 NEA12 IMP04 30 30 30 30 32 30 TOL03 25 30 30 20 30 20

EXAMPLE 25—GENERATION OF DESIGNER N LOLII GENOTYPES BY X-RAY MUTAGENESIS

The generation of designer Neotyphodium endophytes genotypes by X-ray mutagenesis offers the opportunity to create novel endophyte variant strains with enhanced properties, such as enhanced stability in grass hosts, broader host compatibility as well as improved toxin profiles e.g. following elimination of the production of the detrimental alkaloid lolitrem B in the highly stable and broadly compatible ST endophyte.

Such an novel designer endophyte would be advantageous over existing commercial endophytes, such as AR1 and AR37, as it would be highly stable and broadly compatible and with optimal toxin profile.

FIG. 84 shows an experimental work flow for X-ray mutagenesis of endophyte strains.

FIG. 85 shows the indole-diterpene biosynthetic pathway. Lolitrem B is the major toxin that causes ryegrass staggers, a disease of grazing animals. Ten genes in 3 gene clusters are required for lolitrem biosynthesis. We focused initial analysis on 3 Ltm genes, one from each gene cluster. Optimised multiplex PCR analysis was designed and implemented.

EXAMPLE 26—SCREENING OF X-RAY IRRADIATED N. LOLLI STRAINS

In a preliminary primary screen >5,000 colonies of X-ray irradiated N. lolii—established as an initial resource of novel variation of N. lolii endoophytes induced through X-ray mutagenesis and representing a mutagenised N. lolii endophyte strain collection—of were screened by multiplex PCR analysis for the presence of targeted Ltm genes leading to a preliminary identification of ˜140 putative lolitrem B gene cluster PCR-negative colonies (˜2.5% of 5,000 colonies screened). In a secondary screen high quality DNA was extracted (140 liquid cultures) and PCR analysis conducted. This identified 2 putative deletion mutants for one of the lolitrem B genes (Itm J).

EXAMPLE 27—ANTIFUNGAL BIOASSAYS OF DESIGNER X-RAY IRRADIATED N. BORN VARIANT STRAINS

There were eight X-ray irradiated N. lolii variant strains (i.e. X-ray mutagenesis derived variant strains 1-35, 4-7, 7-22, 7-47, 123-20, 124-6, 139-6, 144-16 and 145-15) and one control N. lolii strain (i.e. ST endophyte strain).

Five fungal pathogens (causing a range of fungal diseases and infecting a range of different plant hosts) were included in antifungal bioassays used to analyse the X-ray irradiated N. lolii variant strains, as follows:

-   -   Bipolaris portulacae     -   Colletotrichum graminicola     -   Drechslera brizae     -   Phoma sorghina     -   Rhizoctonia cerealis

No significant difference in antifungal activities of X-ray irradiated N. lolii variant strains tested was observed compared to the spectrum of antifungal activities observed for the control ST endophyte strain.

EXAMPLE 28—IN VITRO GROWTH OF DESIGNER X-RAY IRRADIATED N. LOLII VARIANT STRAINS

Results from the analysis of in vitro growth rate of designer X-ray irradiated N. lolii variant strains are shown in FIG. 86, with a statistical analysis of in vitro growth undertaken at week 5 for the X-irradiated N. lolii variant strains compared to the control ST strain, revealing significant differences in in vitro growth rates as follows: p<0.05* (for X-irradiated N. lolii variant strain 139-6) p<0.01** (for all other mutants)

EXAMPLE 29—GENOME SURVEY SEQUENCING OF DESIGNER X-RAY IRRADIATED N. LOLII VARIANT STRAINS

Eight X-ray irradiated N. lolii ST variant strains and corresponding control ST strain were subjected to genome survey sequencing (GSS), leading to 46-fold to 79-fold genome sequence coverage for the different strains as shown in Table 45.

TABLE 45 Genome sequence coverage obtained in genome survey sequencing for for 8 X-ray irradiated N. lolii ST variant strains and corresponding control ST strain Strain Description Coverage ST ST 23x 139-6 ST irradiated 61x 145-15 ST irradiated 52x 144-16 ST irradiated 46x 1_35 ST irradiated 79x 4_7 ST irradiated 46x 7_22 ST irradiated 53x 7_47 ST irradiated 38x 123-20 ST irradiated 54x 124-6 ST irradiated 75x

EXAMPLE 30—DETECTING GENOME SEQUENCE VARIATION IN DESIGNER X-RAY IRRADIATED N. LOLII VARIANT STRAINS

Results from the analysis to detect genome sequence variation in X-ray irradiated N. lolii variant strains are shown in FIG. 88. Corresponding results on the detection of single nucleotide polymorphisms (SNPs) are shown in FIG. 89 and results on the detection of small insertions/deletions (INDELs) are shown in FIG. 90. Differences in sequence read depth and pair insert size in X-ray irradiated N. lolii variant deletion mutant strains are shown in FIG. 91.

Results on sequence analysis for Ltm gene clusters are shown in FIG. 87. No deletions, large or small, were found in the coding or regulatory sequences of Itm gene clusters. No SNPs, insertions or translocations were found in the coding or regulatory sequences of Itm gene clusters.

EXAMPLE 31—SPECTRUM OF GENOME SEQUENCE CHANGES DETECTED IN THE X-RAY IRRADIATED N. LOLII VARIANT STRAINS

FIG. 92 shows numbers of SNPs detected in genic regions of X-ray irradiated N. lolii variant deletion mutant strains. There are large differences in the number of SNPs detected in the X-ray irradiated N. lolii variant deletion mutant strains and compared to the control ST strain. All X-ray irradiated N. lolii variant deletion mutant strains have over double the number of SNPs per Mb across genic regions compared to the control ST strain. X-ray irradiated N. lolii variant deletion mutant strains have on average 6 SNPs per Mb, where the control ST strain has 2 SNPs per Mb.

FIG. 93 shows numbers of INDELs in genic regions of X-ray irradiated N. lolii variant deletion mutant strains. All X-ray irradiated N. lolii variant deletion mutant strains contain more indels in genic regions than the control ST strain. The difference in indel numbers between the X-ray irradiated N. lolii variant deletion mutant strains and the control ST strain is on average 134 indels per Mb. When grouped by irradiation treatment (i.e. irradiation dose applied and number of repeat irradiations) there appears to be a peak in number of indels at 10Gy*2 treatment, consistent with the results obtained in the SNP detection analysis.

FIG. 94 shows the spectrum of genome sequence changes in the form of deletions detected in X-ray irradiated N. lolii variant deletion mutant strains.

Table 46 shows examples of some of these genome sequence deletions detected in X-ray irradiated N. lolii variant deletion mutant strains.

TABLE 46 Deletions detected in genome sequences of X-ray irradiated N. lolii variant deletion mutant strains. Bold indicates deletions confirmed by changes in sequence read coverage. The remainder are potential transposon deletions. Radiation Strain Treatment Deletion 123_20 30Gy*2 Contig00915 (268 bp) 124_6 30Gy*2 Partial duplication 139_6 30Gy Partial duplication 144_16 30Gy 145_15 30Gy Partial duplication 1_35 10Gy Contig00831 (3.6 kb) 4_7 10Gy 7_22 10Gy*2 7_47 10Gy*2 Contig01131 (0.6 kb), contig01082 (4.2 kb), contig02985 (1 kb), contig02725 (83 bp), contig01095 (130 bp)

The X-ray irradiated N. lolii variant deletion mutant strain #7_47, which was generated following two X-irradiation treatments at 10 Gy dose (10Gy*2) of N. lolii ST endophyte, had the greatest number of large deletions.

EXAMPLE 32—ANNOTATION OF DELETED SEQUENCES IN THE GENOMES OF X-RAY IRRADIATED N. LOLII VARIANT DELETION MUTANT STRAINS X-Ray Irradiated N. Lolii Variant Mutant Strain 1_35:

For the X-ray irradiated N. lolii variant mutant strain 1_35 the following deleted sequences in ST454Contig00831 contig with a ˜4,400-8,000 bp length was detected, with this genome sequence region containing the following two predicted genes:

ST454contig00831_AUGUSTUS_gene_3318:6018 (847 letters) 1) ref |XP_386347.1| hypothetical protein FG06171.1 [Gibberella 660×0.0 gb|EAW12630.1| DUF500 domain protein [Aspergillus NRRL 1]; 253×9e-66, and ST454contig00831_AUGUSTUS_gene_3958:4728 (183 letters); and 2) gb|EAW13545.1| 2,3-cyclic-nucleotide 2-phosphodiesterase [Aspergillus 32×2.4 X-Ray Irradiated N. lolii Variant Mutant Strain 7_47:

For the X-ray irradiated N. lolii variant mutant strain 7_47 the following deleted sequences in ST454Contig01082, ST454Contig01131 and ST454Contig02985, with these genome sequence regions containing no predicted genes:

Query = ST454contig01082 length = 9120 numreads = 287 gb|AAA21442.1|putative pol polyprotein [Magnaporthe grisea] 145 1e−32 Query = ST454contig02985 length = 2414 numreads = 99 gb|AAA21442.1|putative pol polyprotein [Magnaporthe grisea] 92 2e−17

EXAMPLE 33—MUTAGENESIS INDEX OF X-RAY IRRADIATED N. LOLII VARIANT DELETION MUTANT STRAINS

FIG. 95 shows SNPs and Indels per Mb in genic regions of X-ray irradiated N. lolii variant deletion mutant strains derived from X-ray irradiation of N. lolii at different levels of irradiation. Strain 1_35 has a 3.6 kb deletion; Strain 7_47 has 3 deletions (4.2 kb, 1 kb, 0.6 kb in lenght). Strain 124_6 has a partial duplication. Strains 139_6 and 145_15 have partial duplications.

Given that ST endophyte has approximately 443.5 genes per Mb, using 10Gy*2 treatment, the expected rate of SNP/INDEL occurrence is 0.33 per gene in the genome.

Summary

X-ray irradiated N. lolii variant deletion mutant strains were analysed for many types of genome sequence variation i.e. deletions, SNPs, INDELs, inversions and translocations. SNPs, INDELs, deletions and duplications were identified in the genome survey sequences of X-ray irradiated N. lolii variant deletion mutant strains. There was an apparent peak in number of SNPs and INDELs in X-ray irradiated N. lolii variant deletion mutant strains recovered from administering 10Gy*2 X-ray irradiation treatment to N. lolii ST endophyte. The X-ray irradiated N. lolii variant deletion mutant strain 7_47 had 3 large deletions. It was demonstrated that this mutagenesis method based on X-ray irradiation can be used to create novel designer Neotyphodium endophyte strains, and enabled:

-   -   5,000 X-ray irradiated N. lolii variant endophyte strains         derived from X-ray irradiation of ST N. lolii endophyte were         screened;     -   140 putative X-ray irradiated N. lolii variant endophyte mutant         strains were identified;     -   9 X-ray irradiated N. lolii variant endophyte mutant strains         were subjected to antifungal bioassays;     -   9 X-ray X-ray irradiated N. lolii variant endophyte mutant         strains were subjected to in vitro growth assays;     -   9 X-ray irradiated N. lolii variant endophyte mutant strains         were subjected to genome survey sequencing;     -   2 X-ray irradiated N. lolii variant endophyte mutant strains         with gene deletions (1_35 and 7_47) were identified; and     -   3 X-ray irradiated N. lolii variant endophyte mutant strains         with gene duplications (124_6, 139_6 and 145_15) were         identified.

EXAMPLE 34—IN PLANTA ISOGENIC INOCULATION IN PERENNIAL RYEGRASS WITH X-RAY IRRADIATED N. LOLLI VARIANT ENDOPHYTE MUTANT STRAINS

TABLE 47 Isogenic inoculation of perennial ryegrass genotypes (IMP04 and TOL03) with X-ray irradiated N. lolli variant endophyte mutant strains. Numbers indicate number of perennial ryegrass plants of the two genotypes subjected to isogenic inoculation with the different X-ray irradiated N. lolii variant endophyte mutant strains (i.e. ST-IRM 139-6, ST-IRM 145-15, ST-IRM 144-16, ST-IRM 1-35 and ST-IRM 7-47) and control ST endophyte strain. ST-IRM ST-IRM ST-IRM ST-IRM ST-IRM Plant Genotype 139-6 145-15 144-16 1-35 7-47 ST IMP04 30 25 30 30 30 25 TOL03 25 0 25 30 30 20

EXAMPLE 35—METABOLIC PROFILING OF COLCHICINE TREATMENT-DERIVED NEA12DH AND X-RAY IRRADIATION-DERIVED NEOTYPHODIUM VARIANT ENDOPHYTE STRAINS

Results from metabolic profiling of colchicine treatment derived NEA12dh endophyte variant strains is shown in FIG. 96.

Results from metabolic profiling of X-ray irradiation treatment derived N. lolii ST endophyte variant strains is shown in FIG. 97.

The following endophytes were grown on PDB for 3 weeks:

-   -   Control N. lolii ST endophyte strain     -   X-ray irradiation treatment derived N. lolii ST endophyte         variant strain 4-7     -   X-ray irradiation treatment derived N. lolii ST endophyte         variant strain 139-6     -   X-ray irradiation treatment derived N. lolii ST endophyte         variant strain 144-16     -   X-ray irradiation treatment derived N. lolii ST endophyte         variant strain 145-15         and subjected to metabolic profiling using LCMS on corresponding     -   1. Liquid filtrate     -   2. Mycelial extract

The X-ray irradiation treatment derived N. lolii ST endophyte variant strains could be readily distinguished from control N. lolii ST strain using mycelia extracts or filtrates alone.

It will be understood that the invention disclosed and defined in this specification extends to all alternative combinations of two or more of the individual features mentioned or evident from the text or drawings. All of these different combinations constitute various alternative aspects of the invention.

REFERENCES

-   Bouton, J. H., G. C. M. Latch, N. S. Hill, C. S. Hoveland, M. A.     McCann, R. H. Watson, J. A. Parish, L. L. Hawkins and F. N.     Thompson (2002) Agronomy Journal 94(3): 567 574. -   Latch, G. C. M, Christensen, M. J, Tapper, B. A, Easton, H. S,     Hume, D. E, Fletcher, L. R. (2000) U.S. Pat. No. 6,111,170 and     references therein. -   Li, X and Zhang, Y., (2002) Comparative and Functional Genomics 3:     158-160. -   Tapper, B. A, Cooper, B. M, Easton, H. S, Fletcher, L. R, Hume, D.     E, Lane, G. A, Latch, G. C. M, Pennell, C. G. L, Popay, A. J,     Christensen, M. J. (2004) International Patent Application No. WO     2004/106487 and references therein. -   Van Zijll de Jong E, Guthridge K M, Spangenberg G C, Forster J     W (2003) Genome 46 (2): 277-290 -   Young, C. A., Bryant, M. K., Christensen, M. J., Tapper, B. A.,     Bryan, G. T., Scott, B. (2005) Molecular Genetics and Genomics, 274:     13-39. 

1-32. (canceled)
 33. A plant, seed, or part thereof, wherein the plant is a tall fescue or perennial ryegrass plant, wherein the plant, seed, or part thereof is associated with a fungal endophyte isolated from one of tall fescue and perennial ryegrass, said endophyte being selected from the group consisting National Measurement Institute Accession Nos. V10/000002, V10/000003, V10/00004, V10/00001, V10/030284, V10/030285, V12/001413, V12/001414, V12/001415, V12/001416, V12/001417, V12/001418 and V12/001419, and wherein the plant, seed or part thereof is associated with a fungal endophyte isolated from a different type of plant to form an association that does not occur in nature.
 34. The plant, seed, or part thereof according to claim 33, wherein said plant is a tall fescue, the plant, seed, or part thereof is associated with an endophyte selected from the group consisting of National Measurement Institute Accession Nos. V10/000002, V10/000003, and V10/00004.
 35. The plant, seed, or part thereof according to claim 33, wherein said plant is a perennial ryegrass plant, the plant, seed, or part thereof and is associated with an endophyte selected from the group consisting of National Measurement Institute Accession Nos. V10/00001, V10/030284, V10/030285, V12/001413, V12/001414, V12/001415, V12/001416, V12/001417, V12/001418 and V12/001419. 